Genetic Encoding of Phosphorylated Amino Acids into Proteins.

Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea.

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.

Subchondral rafting wires reduce tibial plateau fracture subsidence.

PURPOSE: To determine if subchondral rafting wires retained as adjunctive tibial plateau fracture fixation affect postoperative articular subsidence. METHODS: A retrospective cohort study was conducted at one Level 1 trauma center and one academic university hospital. Consecutive adults with closed, displaced OTA/AO 41B/C tibial plateau fractures treated between 2018 and 2023 with open reduction internal fixation were included. Patients who were not ambulatory, with contralateral injuries limiting weight bearing, and without follow-up radiographs of the injured extremity were excluded. The intervention was retention of subchondral rafting wires as definitive fixation. The primary outcome was linear articular surface subsidence between postoperative and follow-up AP knee radiographs. Linear subsidence was compared between groups using Welch's two sample t test. Associations of linear subsidence with patient, injury, and treatment characteristics were assessed by multivariable linear regression. RESULTS: We identified 179 patients of a mean age of 44 ± 14 years, of whom 15 (8.4%) received subchondral rafting wires. Median follow-up was 121 days. No patients who received rafting wires as definitive implants experienced linear subsidence ≥ 2 mm, while 22 patients (13.4%) who did not receive rafting wires experienced linear subsidence ≥ 2 mm (p = 0.130). Subchondral rafting wires were associated with less linear subsidence (0.3 mm [95% confidence interval - 0.3-0.9 mm] vsersus 1.0 mm [- 0.9-2.9 mm], p < 0.001). The depth of linear subsidence was significantly associated on multivariable regression with male sex, depressed plateau area, active smoking, and retained rafting wires. CONCLUSION: Subchondral rafting wires were associated with a small reduction in articular subsidence after internal fixation of tibial plateau fractures. Routine rafting wires may be useful for patients and fractures at high risk of articular subsidence.

The modulatory role of gut microbiota on host behavior: exploring the interaction between the brain-gut axis and the neuroendocrine system.

The brain-gut axis refers to the communication between the central nervous system and the gastrointestinal tract, with the gut microbiome playing a crucial role. While our understanding of the interaction between the gut microbiome and the host's physiology is still in its nascent stage, evidence suggests that the gut microbiota can indeed modulate host behavior. Understanding the specific mechanisms by which the gut microbiota community modulates the host's behavior remains the focus of present and future neuro-gastroenterology studies. This paper reviews several pieces of evidence from the literature on the impact of gut microbiota on host behavior across animal taxa. We explore the different pathways through which this modulation occurs, with the aim of deepening our understanding of the fascinating relationship between the gut microbiome and the central nervous system.

Suppression of host humoral immunity by Borrelia burgdorferi varies over the course of infection.

Borrelia burgdorferi, the spirochetal agent of Lyme disease, utilizes a variety of strategies to evade and suppress the host immune response, which enables it to chronically persist in the host. The resulting immune response is characterized by unusually strong IgM production and a lack of long-term protective immunity. Previous studies in mice have shown that infection with B. burgdorferi also broadly suppresses host antibody responses against unrelated antigens. Here, we show that mice infected with B. burgdorferi and concomitantly immunized with recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein had an abrogated antibody response to the immunization. To further define how long this humoral immune suppression lasts, mice were immunized at 2, 4, and 6 weeks post-infection. Suppression of host antibody production against the SARS-CoV-2 spike protein peaked at 2 weeks post-infection but continued for all timepoints measured. Antibody responses against the SARS-CoV-2 spike protein were also assessed following antibiotic treatment to determine whether this immune suppression persists or resolves following clearance of B. burgdorferi. Host antibody production against the SARS-CoV-2 spike protein returned to baseline following antibiotic treatment; however, anti-SARS-CoV-2 IgM remained high, comparable to levels found in B. burgdorferi-infected but untreated mice. Thus, our data demonstrate restored IgG responses following antibiotic treatment but persistently elevated IgM levels, indicating lingering effects of B. burgdorferi infection on the immune system following treatment.

Nodal positivity in patients with clinically and radiologically node-negative breast cancer treated with neoadjuvant chemotherapy: multicentre collaborative study.

BACKGROUND: The necessity of performing a sentinel lymph node biopsy in patients with clinically and radiologically node-negative breast cancer after neoadjuvant chemotherapy has been questioned. The aim of this study was to determine the rate of nodal positivity in these patients and to identify clinicopathological features associated with lymph node metastasis after neoadjuvant chemotherapy (ypN+). METHODS: A retrospective multicentre study was performed. Patients with cT1-3 cN0 breast cancer who underwent sentinel lymph node biopsy after neoadjuvant chemotherapy between 2016 and 2021 were included. Negative nodal status was defined as the absence of palpable lymph nodes, and the absence of suspicious nodes on axillary ultrasonography, or the absence of tumour cells on axillary nodal fine needle aspiration or core biopsy. RESULTS: A total of 371 patients were analysed. Overall, 47 patients (12.7%) had a positive sentinel lymph node biopsy. Nodal positivity was identified in 22 patients (29.0%) with hormone receptor+/human epidermal growth factor receptor 2- tumours, 12 patients (13.8%) with hormone receptor+/human epidermal growth factor receptor 2+ tumours, 3 patients (5.6%) with hormone receptor-/human epidermal growth factor receptor 2+ tumours, and 10 patients (6.5%) with triple-negative breast cancer. Multivariable logistic regression analysis showed that multicentric disease was associated with a higher likelihood of ypN+ (OR 2.66, 95% c.i. 1.18 to 6.01; P = 0.018), whilst a radiological complete response in the breast was associated with a reduced likelihood of ypN+ (OR 0.10, 95% c.i. 0.02 to 0.42; P = 0.002), regardless of molecular subtype. Only 3% of patients who had a radiological complete response in the breast were ypN+. The majority of patients (85%) with a positive sentinel node proceeded to axillary lymph node dissection and 93% had N1 disease. CONCLUSION: The rate of sentinel lymph node positivity in patients who achieve a radiological complete response in the breast is exceptionally low for all molecular subtypes.

First impressions: A prospective evaluation of patient-physician concordance and satisfaction following the initial medical oncology consultation.

BACKGROUND: An especially significant event in the patient-oncologist relationship is the initial consultation, where many complex topics-diagnosis, treatment intent, and often, prognosis-are discussed in a relatively short period of time. This study aimed to measure patients' understanding of the information discussed during their first medical oncology visit and their satisfaction with the communication from medical oncologists. METHODS: Between January and August 2021, patients without prior systemic treatment of their gastrointestinal malignancy (GI) attending the Princess Margaret Cancer Centre (PMCC) were approached within 24 h of their initial consultation to complete a paper-based questionnaire assessing understanding of their disease (diagnosis, treatment plan/intent, and prognosis) and satisfaction with the consultation. Medical oncology physicians simultaneously completed a similar questionnaire about the information discussed at the initial visit. Matched patient-physician responses were compared to assess the degree of concordance. RESULTS: A total of 184 matched patient-physician surveys were completed. The concordance rates for understanding of diagnosis, treatment plan, treatment intent, and prognosis were 92.9%, 59.2%, 66.8%, and 59.8%, respectively. After adjusting for patient and physician variables, patients who reported treatment intent to be unclear at the time of the consultation were independently associated with lower satisfaction scores (global p = 0.014). There was no statistically significant association between patient satisfaction and whether prognosis was disclosed (p = 0.08). CONCLUSION: An in-depth conversation as to what treatment intent and prognosis means is reasonable during the initial medical oncology consultation to ensure patients and caregivers have a better understanding about their cancer.

Leaf-cutter ants - mycorrhizal fungi: observations and research questions from an unexpected mutualism.

Leaf-cutter ants (LCAs) are widely distributed and alter the physical and biotic architecture above and below ground. In neotropical rainforests, they create aboveground and belowground disturbance gaps that facilitate oxygen and carbon dioxide exchange. Within the hyperdiverse neotropical rainforests, arbuscular mycorrhizal (AM) fungi occupy nearly all of the forest floor. Nearly every cubic centimeter of soil contains a network of hyphae of Glomeromycotina, fungi that form arbuscular mycorrhizae. Our broad question is as follows: how can alternative mycorrhizae, which are-especially ectomycorrhizae-essential for the survival of some plant species, become established? Specifically, is there an ant-mycorrhizal fungus interaction that facilitates their establishment in these hyperdiverse ecosystems? In one lowland Costa Rican rainforest, nests of the LCA Atta cephalotes cover approximately 1.2% of the land surface that is broadly scattered throughout the forest. On sequencing the DNA from soil organisms, we found the inocula of many AM fungi in their nests, but the nests also contained the inocula of ectomycorrhizal, orchid mycorrhizal, and ericoid mycorrhizal fungi, including Scleroderma sinnamariense, a fungus critical to Gnetum leyboldii, an obligate ectomycorrhizal plant. When the nests were abandoned, new root growth into the nest offered opportunities for new mycorrhizal associations to develop. Thus, the patches created by LCAs appear to be crucial sites for the establishment and survival of shifting mycorrhizal plant-fungal associations, in turn facilitating the high diversity of these communities. A better understanding of the interactions of organisms, including cross-kingdom and ant-mycorrhizal fungal interactions, would improve our understanding of how these ecosystems might tolerate environmental change.

A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice.

The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.

Collaborative Use of Sensor Networks and Cyberinfrastructure to Understand Complex Ecosystem Interactions in a Tropical Rainforest: Challenges and Lessons Learned.

Collaborations between ecosystem ecologists and engineers have led to impressive progress in developing complex models of biogeochemical fluxes in response to global climate change. Ecology and engineering iteratively inform and transform each other in these efforts. Nested data streams from local sources, adjacent networks, and remote sensing sources together magnify the capacity of ecosystem ecologists to observe systems in near real-time and address questions at temporal and spatial scales that were previously unobtainable. We describe our research experiences working in a Costa Rican rainforest ecosystem with the challenges presented by constant high humidity, 4300 mm of annual rainfall, flooding, small invertebrates entering the tiniest openings, stinging insects, and venomous snakes. Over the past two decades, we faced multiple challenges and learned from our mistakes to develop a broad program of ecosystem research at multiple levels of integration. This program involved integrated networks of diverse sensors on a series of canopy towers linked to multiple belowground soil sensor arrays that could transport sensor data streams from the forest directly to an off-site location via a fiber optic cable. In our commentary, we highlight three components of our work: (1) the eddy flux measurements using canopy towers; (2) the soil sensor arrays for measuring the spatial and temporal patterns of CO2 and O2 fluxes at the soil-atmosphere interface; and (3) focused investigations of the ecosystem impact of leaf-cutter ants as "ecosystem engineers" on carbon fluxes.

Time to complete contemporary dental procedures - estimates from a cross-sectional survey of the dental team.

BACKGROUND: There are few contemporary studies on the time taken to complete dental procedures, those most heavily relied on in the United Kingdom date back to 1999. OBJECTIVES: This work aimed to establish how long members of the dental team took to complete specific dental procedures, relevant to their scope of practice. METHODS: Data were collected via a purposive sample of 96 dentists, dental hygienists/therapists and dental nurses. Via an online survey, participants were asked to state the mean, minimum and maximum time they estimated that they took to complete individual dental procedures. RESULTS: The mean time taken to complete procedures common to both dentists and dental hygienists/therapists ranged from 3.7 to 4 min respectively for clinical note reading prior to seeing patients to 30.1 and 28 min to undertake root surface debridement. There were no significant differences between the time taken by dentists and dental hygienists/therapists to treat adult patients. However, in all but one procedure, dental hygienists/therapists reported taking longer (p = 0.04) to treat child patients. CONCLUSIONS: The data provided here represent an up to date assessment of the time taken to complete specific tasks by different members of the dental team. These data will be of value to service planners and commissioners interested in evolving a dental care system that employs a greater degree of skill-mix and preventively oriented care.

An impact evaluation of conservation investments targeting long-distance migratory species.

We evaluated the impact of a philanthropic program investing in the conservation of sites along the Pacific Americas Flyway, which spans >16,000 km of coastline and is used by millions of shorebirds. Using a quasi-experimental, mixed methods approach, we estimated what would have happened to shorebird populations at 17 wintering sites without the sustained and additional investment they received. We modeled shorebird populations across the entire flyway and at sites with and without investment. Combining shorebird abundance estimates with a land-cover classification model, we used the synthetic control method to create counterfactuals for shorebird trends at the treatment sites. We found no evidence of an overall effect across three outcome variables. Species- and site-level treatment effects were heterogeneous, with a few cases showing evidence of a positive effect, including a site with a high level of overall investment. Results suggest six shorebirds declined across the entire flyway, including at many Latin American sites. However, the percentage of flyway populations present at the sites remained stable, and the percentage at the treatment sites was higher (i.e., investment sites) than at control sites. Multiple mechanisms behind our results are possible, including that investments have yet to mitigate impacts and negative impacts at other sites are driving declines at the treatment sites. A limitation of our evaluation is the sole focus on shorebird abundance and the lack of data that prohibits the inclusion of other outcome variables. Monitoring infrastructure is now in place to design a more robust and a priori shorebird evaluation framework across the entire flyway. With this framework, it will prove easier to prioritize limited dollars to result in the most positive conservation outcomes.

Evaluación del impacto de la inversión para la conservación enfocada en especies migratorias de largo recorrido Resumen Evaluamos el impacto de un programa filantrópico que invierte en la conservación de sitios a lo largo de la Ruta Migratoria Pacífico-Américas, la cual abarca >16,000 km de la línea costera y millones de aves playeras la usan. Estimamos con una estrategia cuasiexperimental y de métodos mixtos lo que habría pasado con las poblaciones de estas aves en 17 sitios invernales sin la inversión adicional y continua que recibieron. Modelamos estas poblaciones en toda la ruta y en sitios con y sin inversión. Combinamos las estimaciones de aves playeras con el modelo de clasificación de la cobertura del suelo y usamos el método de control sintético para crear contrafactuales para las tendencias de las aves playeras en sitios de tratamiento. No encontramos evidencia alguna de un efecto generalizado en las tres variables de los resultados. Los efectos del tratamiento de especies y de sitio fueron heterogéneos, con unos cuantos casos que mostraron evidencia de un efecto positivo, incluido un sitio con un nivel elevado de inversión general. Los resultados sugieren que seis especies de aves playeras declinaron a lo largo de toda la ruta, incluyendo en varios sitios de América Latina. Sin embargo, el porcentaje de poblaciones de la ruta presentes en los sitios permaneció estable y el porcentaje en los sitios de tratamiento (sitios de inversión) fue más elevado que en los sitios control. Muchos mecanismos son posibles detrás de nuestros resultados, incluidas las inversiones que todavía no han mitigado impactos y los impactos negativos en otros sitios que están causando las declinaciones en los sitios de tratamiento. Una limitación en nuestra evaluación es el enfoque único en la abundancia de aves playeras y la falta de datos que impiden la inclusión de otras variables de los resultados. El monitoreo de la infraestructura ahora está en una posición en la que puede diseñar un marco de evaluación más robusto y a priori de las aves playeras a lo largo de toda la ruta. Con este marco, será más fácil priorizar los dólares limitados para que los resultados de conservación sean lo más positivos posible.

Predictive modelling of response to neoadjuvant therapy in HER2+ breast cancer.

HER2-positive (HER2+) breast cancer accounts for 20-25% of all breast cancers. Predictive biomarkers of neoadjuvant therapy response are needed to better identify patients with early stage disease who may benefit from tailored treatments in the adjuvant setting. As part of the TCHL phase-II clinical trial (ICORG10-05/NCT01485926) whole exome DNA sequencing was carried out on normal-tumour pairs collected from 22 patients. Here we report predictive modelling of neoadjuvant therapy response using clinicopathological and genomic features of pre-treatment tumour biopsies identified age, estrogen receptor (ER) status and level of immune cell infiltration may together be important for predicting response. Clonal evolution analysis of longitudinally collected tumour samples show subclonal diversity and dynamics are evident with potential therapy resistant subclones detected. The sources of greater pre-treatment immunogenicity associated with a pathological complete response is largely unexplored in HER2+ tumours. However, here we point to the possibility of APOBEC associated mutagenesis, specifically in the ER-neg/HER2+ subtype as a potential mediator of this immunogenic phenotype.

Does Suicide Risk Screening Improve the Identification of Primary Care Patients Who Will Attempt Suicide Versus Depression Screening Alone?

OBJECTIVE: The effectiveness of suicide risk screening relative to depression screening alone among primary care patients has not been tested rigorously. This study compared the performance of multiple depression screening methods (Patient Health Questionnaire [PHQ]-2, PHQ-8, and PHQ-9) and multiple suicide risk screening methods (PHQ-9 item 9 and suicide-focused screening of "thoughts of killing yourself" during the entire lifespan, within the past month, and within the past week) in a convenience sample of primary care patients. METHODS: A total of 2,744 patients (military personnel, family members, and retirees) from six military primary care clinics completed the PHQ-9 and screening for suicidal ideation (SI) during routine clinic visits. Follow-up phone interviews were conducted for one year post-baseline to assess the incidence of suicide attempts, the study's primary outcome. Sensitivity, specificity, accuracy, and F1 statistics were calculated for each screening method for identifying patients who attempted suicide. RESULTS: More than 65% of patients who screened positive for SI also screened positive for depression on the PHQ-9. Depression screening with the PHQ-9 correctly identified more patients who attempted suicide during follow-up than the PHQ-2, past week SI, and past month SI. The PHQ-9 correctly identified more patients who attempted suicide within 3 months than lifetime SI, but lifetime SI correctly identified more patients who attempted suicide within 6 and 12 months. CONCLUSION: Depression screening with the PHQ-9 was the most effective strategy for identifying patients who attempted suicide in the near term. Universal suicide risk screening is unlikely to meaningfully improve identification of higher-risk patients beyond PHQ-9 depression screening.

The Role of Time Perspective and Mindfulness on Life Satisfaction in the United States of America, Spain, Poland and Japan: A Cross-Cultural Study.

We assessed the cross-cultural role of Time Perspective (TP) tendencies [Past Positive (PP), Past Negative (PN), Present Hedonistic (PH), Present Fatalistic (PF), and Future (F)], the Deviation from a Balanced Time Perspective (DBTP) profile, the Deviation from a Negative Time Perspective (DNTP) profile, and mindfulness on life satisfaction (LS). The sample consisted of psychology undergraduate students (N= 867, MAGE= 20.19, SD= 3.417) in four countries: USA, Spain, Poland and Japan. We used a 17-item short version of the Zimbardo Time Perspective Inventory (ZTPI), the Mindful Attention Awareness Scale (MAAS), and the Satisfaction with Life Scale (SWLS) in all countries. For ensuring measurement invariance, we conducted pairwise CFAs for the ZTPI-17, MAAS and SWLS. Regression analyses showed that PN predicted decreased LS in Poland and Japan. PP predicted increased LS in Spain. F predicted increased LS in Poland. DNTP predicted decreased LS in Poland. Mindfulness predicted decreased LS in Japan and increased LS in USA, Spain and Poland. Moreover, mediation analyses revealed that the DBTP partially mediated the relationship between mindfulness and LS in Spain and USA. The DNTP partially mediated the relationship between mindfulness and LS in Spain, Poland and Japan (opposite direction). The findings suggest that the association of TP, mindfulness and LS differs across the investigated countries as a function of culture.

Performance of GAP and ILD-GAP models in predicting lung transplant or death in interstitial pneumonia with autoimmune features.

OBJECTIVES: To assess the ability of two risk prediction models in interstitial lung disease (ILD) to predict death or lung transplantation in a cohort of patients with interstitial pneumonia with autoimmune features (IPAF). METHODS: We performed a retrospective cohort study of adults with IPAF at an academic medical center. The primary outcome was a composite of lung transplantation or death. We applied the patient data to the previously described GAP and ILD-GAP models to determine the ability of these models to predict the composite outcome. Model discrimination was assessed using the c-index, and model calibration was determined by comparing the incidence ratios of observed versus expected deaths. RESULTS: Ninety-four patients with IPAF were included. Mean (standard deviation) age was 58 (13.5) years and the majority were female (62%). The majority met serologic and morphologic criteria for IPAF (94% and 91%, respectively). The GAP model had a c-index of 0.664 (95% confidence interval [CI] 0.547-0.781), while the ILD-GAP model had a c-index of 0.569 (95% CI 0.440-0.697). In those with GAP stage 1 or GAP stage 2 disease, calibration of the GAP model was satisfactory at 2 and 3 years for the cumulative end point of lung transplantation or death. CONCLUSION: In patients with IPAF, the GAP model performed well as a predictor of lung transplantation or death at 2 years and 3 years from ILD diagnosis in patients with GAP stage 1 and GAP stage 2 disease.

Combination of clinical, radiomic, and "delta" radiomic features in survival prediction of metastatic gastroesophageal adenocarcinoma.

Objectives: To identify combined clinical, radiomic, and delta-radiomic features in metastatic gastroesophageal adenocarcinomas (GEAs) that may predict survival outcomes. Methods: A total of 166 patients with metastatic GEAs on palliative chemotherapy with baseline and treatment/follow-up (8-12 weeks) contrast-enhanced CT were retrospectively identified. Demographic and clinical data were collected. Three-dimensional whole-lesional radiomic analysis was performed on the treatment/follow-up scans. "Delta" radiomic features were calculated based on the change in radiomic parameters compared to the baseline. The univariable analysis (UVA) Cox proportional hazards model was used to select clinical variables predictive of overall survival (OS) and progression-free survival (PFS) (p-value <0.05). The radiomic and "delta" features were then assessed in a multivariable analysis (MVA) Cox model in combination with clinical features identified on UVA. Features with a p-value <0.01 in the MVA models were selected to assess their pairwise correlation. Only non-highly correlated features (Pearson's correlation coefficient <0.7) were included in the final model. Leave-one-out cross-validation method was used, and the 1-year area under the receiver operating characteristic curve (AUC) was calculated for PFS and OS. Results: Of the 166 patients (median age of 59.8 years), 114 (69%) were male, 139 (84%) were non-Asian, and 147 (89%) had an Eastern Cooperative Oncology Group (ECOG) performance status of 0-1. The median PFS and OS on treatment were 3.6 months (95% CI 2.86, 4.63) and 9 months (95% CI 7.49, 11.04), respectively. On UVA, the number of chemotherapy cycles and number of lesions at the end of treatment were associated with both PFS and OS (p < 0.001). ECOG status was associated with OS (p = 0.0063), but not PFS (p = 0.054). Of the delta-radiomic features, delta conventional HUmin, delta gray-level zone length matrix (GLZLM) GLNU, and delta GLZLM LGZE were incorporated into the model for PFS, and delta shape compacity was incorporated in the model for OS. Of the treatment/follow-up radiomic features, shape compacity and neighborhood gray-level dependence matrix (NGLDM) contrast were used in both models. The combined 1-year AUC (Kaplan-Meier estimator) was 0.82 and 0.81 for PFS and OS, respectively. Conclusions: A combination of clinical, radiomics, and delta-radiomic features may predict PFS and OS in GEAs with reasonable accuracy.

What would other emergency stroke teams do? Using explainable machine learning to understand variation in thrombolysis practice.

INTRODUCTION: The aim of this work was to understand between-hospital variation in thrombolysis use among emergency stroke admissions in England and Wales. PATIENTS: A total of 88,928 patients who arrived at all 132 emergency stroke hospitals in England Wales within 4 h of stroke onset, from 2016 to 2018. METHODS: Machine learning was applied to the Sentinel Stroke National Audit Programme (SSNAP) data set, to learn which patients in each hospital would likely receive thrombolysis. We used XGBoost machine learning models, coupled with a SHAP model for explainability; Shapley (SHAP) values, providing estimates of how patient features, and hospital identity, influence the odds of receiving thrombolysis. RESULTS: Thrombolysis use in patients arriving within 4 h of known or estimated stroke onset ranged 7% -49% between hospitals. The odds of receiving thrombolysis reduced 9-fold over the first 120 min of arrival-to-scan time, varied 30-fold with stroke severity, reduced 3-fold with estimated rather than precise stroke onset time, fell 6-fold with increasing pre-stroke disability, fell 4-fold with onset during sleep, fell 5-fold with use of anticoagulants, fell 2-fold between 80 and 110 years of age, reduced 3-fold between 120 and 240 min of onset-to-arrival time and varied 13-fold between hospitals. The majority of between-hospital variance was explained by the hospital, rather than the differences in local patient populations. CONCLUSIONS: Using explainable machine learning, we identified that the majority of the between-hospital variation in thrombolysis use in England and Wales may be explained by differences in in-hospital processes and differences in attitudes to judging suitability for thrombolysis.

Forecasting the daily demand for emergency medical ambulances in England and Wales: a benchmark model and external validation.

BACKGROUND: We aimed to select and externally validate a benchmark method for emergency ambulance services to use to forecast the daily number of calls that result in the dispatch of one or more ambulances. METHODS: The study was conducted using standard methods known to the UK's NHS to aid implementation in practice. We selected our benchmark model from a naive benchmark and 14 standard forecasting methods. Mean absolute scaled error and 80 and 95% prediction interval coverage over a 84 day horizon were evaluated using time series cross validation across eight time series from the South West of England. External validation was conducted by time series cross validation across 13 time series from London, Yorkshire and Welsh Ambulance Services. RESULTS: A model combining a simple average of Facebook's prophet and regression with ARIMA errors (1, 1, 3)(1, 0, 1, 7) was selected. Benchmark MASE, 80 and 95% prediction intervals were 0.68 (95% CI 0.67 - 0.69), 0.847 (95% CI 0.843 - 0.851), and 0.965 (95% CI 0.949 - 0.977), respectively. Performance in the validation set was within expected ranges for MASE, 0.73 (95% CI 0.72 - 0.74) 80% coverage (0.833; 95% CI 0.828-0.838), and 95% coverage (0.965; 95% CI 0.963-0.967). CONCLUSIONS: We provide a robust externally validated benchmark for future ambulance demand forecasting studies to improve on. Our benchmark forecasting model is high quality and usable by ambulance services. We provide a simple python framework to aid its implementation in practice. The results of this study were implemented in the South West of England.

Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes.

The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.