Energy in Newtonian gravity

In Newtonian gravity it is a moot question whether energy should be localized in the field or inside matter. An argument from relativity suggests a compromise in which the contribution from the field in vacuum is positive definite. We show that the same compromise is implied by Noether's theorem applied to a variational principle for perfect fluids, if we assume Dirichlet boundary conditions on the potential. We then analyse a thought experiment due to Bondi and McCrea that gives a clean example of inductive energy transfer by gravity. Some history of the problem is includedComment: Version 2 has 18 pages, and was much improved by referee

Prostate Age Gap: An MRI Surrogate Marker of Aging for Prostate Cancer Detection

Background Aging is the most important risk factor for prostate cancer (PC). Imaging techniques can be useful to measure age-related changes associated with the transition to diverse pathological states. However, biomarkers of aging from prostate magnetic resonance imaging (MRI) remain to be explored. Purpose To develop an aging biomarker from prostate MRI and to examine its relationship with clinically significant PC (csPC, Gleason score ≥7) risk occurrence. Study Type Retrospective. Population Four hundred and sixty-eight (65.97 ± 6.91 years) biopsied males, contributing 7243 prostate MRI slices. A deep learning (DL) model was trained on 3223 MRI slices from 81 low-grade PC (Gleason score ≤6) and 131 negative patients, defined as non-csPC. The model was tested on 90 negative, 52 low-grade (142 non-csPC), and 114 csPC patients. Field Strength/Sequence 3-T, axial T2-weighted spin sequence. Assessment Chronological age was defined as the age of the participant at the time of the visit. Prostate-specific antigen (PSA), prostate volume, Gleason, and Prostate Imaging-Reporting and Data System (PI-RADS) scores were also obtained. Manually annotated prostate masks were used to crop the MRI slices, and a DL model was trained with those from non-csPC patients to estimate the age of the patients. Following, we obtained the prostate age gap (PAG) on previously unseen csPC and non-csPC cropped MRI exams. PAG was defined as the estimated model age minus the patient's age. Finally, the relationship between PAG and csPC risk occurrence was assessed through an adjusted multivariate logistic regression by PSA levels, age, prostate volume, and PI-RADS ≥ 3 score. Statistical Tests T-test, Mann–Whitney U test, permutation test, receiver operating characteristics (ROC), area under the curve (AUC), and odds ratio (OR). A P value <0.05 was considered statistically significant. Results After adjusting, there was a significant difference in the odds of csPC (OR = 3.78, 95% confidence interval [CI]: 2.32–6.16). Further, PAG showed a significantly larger bootstrapped AUC to discriminate between csPC and non-csPC than that of adjusted PI-RADS ≥ 3 (AUC = 0.981, 95% CI: 0.975–0.987).publishedVersio

Leveraging multi-view data without annotations for prostate MRI segmentation: A contrastive approach

An accurate prostate delineation and volume characterization can support the clinical assessment of prostate cancer. A large amount of automatic prostate segmentation tools consider exclusively the axial MRI direction in spite of the availability as per acquisition protocols of multi-view data. Further, when multi-view data is exploited, manual annotations and availability at test time for all the views is commonly assumed. In this work, we explore a contrastive approach at training time to leverage multi-view data without annotations and provide flexibility at deployment time in the event of missing views. We propose a triplet encoder and single decoder network based on U-Net, tU-Net (triplet U-Net). Our proposed architecture is able to exploit non-annotated sagittal and coronal views via contrastive learning to improve the segmentation from a volumetric perspective. For that purpose, we introduce the concept of inter-view similarity in the latent space. To guide the training, we combine a dice score loss calculated with respect to the axial view and its manual annotations together with a multi-view contrastive loss. tU-Net shows statistical improvement in dice score coefficient (DSC) with respect to only axial view (91.25+-0.52% compared to 86.40+-1.50%,P<.001). Sensitivity analysis reveals the volumetric positive impact of the contrastive loss when paired with tU-Net (2.85+-1.34% compared to 3.81+-1.88%,P<.001). Further, our approach shows good external volumetric generalization in an in-house dataset when tested with multi-view data (2.76+-1.89% compared to 3.92+-3.31%,P=.002), showing the feasibility of exploiting non-annotated multi-view data through contrastive learning whilst providing flexibility at deployment in the event of missing views.Comment: Under revie

Prostate Cancer IRE Study (PRIS): A Randomized Controlled Trial Comparing Focal Therapy to Radical Treatment in Localized Prostate Cancer

The aim of focal treatments (FTs) in prostate cancer (PCa) is to treat lesions while preserving surrounding benign tissue and anatomic structures. Irreversible electroporation (IRE) is a nonthermal technique that uses high-voltage electric pulses to increase membrane permeability and induce membrane disruption in cells, which potentially causes less damage to the surrounding tissue in comparison to other ablative techniques. We summarize the study protocol for the Prostate Cancer IRE Study (PRIS), which involves two parallel randomized controlled trials comparing IRE with (1) robot-assisted radical prostatectomy (RARP) or (2) radiotherapy in men with newly diagnosed intermediate-risk PCa (NCT05513443). To reduce the number of patients for inclusion and the study duration, the primary outcomes are functional outcomes: urinary incontinence in study 1 and irritative urinary symptoms in study 2. Providing evidence of the lower impact of IRE on functional outcomes will lay a foundation for the design of future multicenter studies with an oncological outcome as the primary endpoint. Erectile function, quality of life, treatment failure, adverse events, and cost effectiveness will be evaluated as secondary objectives. Patients diagnosed with Gleason score 3 + 4 or 4 + 3 PCa from a single lesion visible on magnetic resonance imaging (MRI) without any Gleason grade 4 or higher in systematic biopsies outside of the target (unifocal significant disease), aged ≥40 yr, with no established extraprostatic extension on multiparametric MRI, a lesion volume of <1.5 cm3, prostate-specific antigen <20 ng/ml, and stage ≤T2b are eligible for inclusion. The study plan is to recruit 184 men

Biochemical Recurrence and Risk of Mortality Following Radiotherapy or Radical Prostatectomy

Importance: Stratifying patients with biochemical recurrence (BCR) after primary treatment for prostate cancer based on the risk of prostate cancer-specific mortality (PCSM) is essential for determining the need for further testing and treatments. Objective: To evaluate the association of BCR after radical prostatectomy or radiotherapy and its current risk stratification with PCSM. Design, Setting, and Participants: This population-based cohort study included a total of 16 311 male patients with 10 364 (64%) undergoing radical prostatectomy and 5947 (36%) undergoing radiotherapy with curative intent (cT1-3, cM0) and PSA follow-up in Stockholm, Sweden, between 2003 and 2019. Follow-up for all patients was until death, emigration, or end of the study (ie, December 31, 2018). Data were analyzed between September 2022 and March 2023. Main Outcomes and Measures: Primary outcomes of the study were the cumulative incidence of BCR and PCSM. Patients with BCR were stratified in low- and high-risk according to European Association of Urology (EAU) criteria. Exposures: Radical prostatectomy or radiotherapy. Results: A total of 16 311 patients were included. Median (IQR) age was 64 (59-68) years in the radical prostatectomy cohort (10 364 patients) and 69 (64-73) years in the radiotherapy cohort (5947 patients). Median (IQR) follow-up for survivors was 88 (55-138) months and 89 (53-134) months, respectively. Following radical prostatectomy, the 15-year cumulative incidences of BCR were 16% (95% CI, 15%-18%) for the 4024 patients in the low D'Amico risk group, 30% (95% CI, 27%-32%) for the 5239 patients in the intermediate D'Amico risk group, and 46% (95% CI, 42%-51%) for 1101 patients in the high D'Amico risk group. Following radiotherapy, the 15-year cumulative incidences of BCR were 18% (95% CI, 15%-21%) for the 1230 patients in the low-risk group, 24% (95% CI, 21%-26%) for the 2355 patients in the intermediate-risk group, and 36% (95% CI, 33%-39%) for the 2362 patients in the high-risk group. The 10-year cumulative incidences of PCSM after radical prostatectomy were 4% (95% CI, 2%-6%) for the 1101 patients who developed low-risk EAU-BCR and 9% (95% CI, 5%-13%) for 649 patients who developed high-risk EAU-BCR. After radiotherapy, the 10-year PCSM cumulative incidences were 24% (95% CI, 19%-29%) for the 591 patients in the low-risk EAU-BCR category and 46% (95% CI, 40%-51%) for the 600 patients in the high-risk EAU-BCR category. Conclusions and Relevance: These findings suggest the validity of EAU-BCR stratification system. However, while the risk of dying from prostate cancer in low-risk EAU-BCR after radical prostatectomy was very low, patients who developed low-risk EAU-BCR after radiotherapy had a nonnegligible risk of prostate cancer mortality. Improving risk stratification of patients with BCR is pivotal to guide salvage treatment decisions, reduce overtreatment, and limit the number of staging tests in the event of PSA elevations after primary treatment.</p

Melting Domain Size and Recrystallization Dynamics of Ice Revealed by Time-Resolved X-ray Scattering

The phase transition between water and ice is ubiquitous and one of the most important phenomena in nature. Here, we performed time-resolved x-ray scattering experiments capturing the melting and recrystallization dynamics of ice. The ultrafast heating of ice I is induced by an IR laser pulse and probed with an intense x-ray pulse, which provided us with direct structural information on different length scales. From the wide-angle x-ray scattering (WAXS) patterns, the molten fraction, as well as the corresponding temperature at each delay, were determined. The small-angle x-ray scattering (SAXS) patterns, together with the information extracted from the WAXS analysis, provided the time-dependent change of the size and the number of the liquid domains. The results show partial melting (~13 %) and superheating of ice occurring at around 20 ns. After 100 ns, the average size of the liquid domains grows from about 2.5 nm to 4.5 nm by the coalescence of approximately six adjacent domains. Subsequently, we capture the recrystallization of the liquid domains, which occurs on microsecond timescales due to the cooling by heat dissipation and results to a decrease of the average liquid domain size

Bioclipse: an open source workbench for chemo- and bioinformatics

BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at

Carbon nanotubes allow capture of krypton, barium and lead for multichannel biological X-ray fluorescence imaging

The desire to study biology in situ has been aided by many imaging techniques. Among these, X-ray fluorescence (XRF) mapping permits observation of elemental distributions in a multichannel manner. However, XRF imaging is underused, in part, because of the difficulty in interpreting maps without an underlying cellular ‘blueprint’; this could be supplied using contrast agents. Carbon nanotubes (CNTs) can be filled with a wide range of inorganic materials, and thus can be used as ‘contrast agents’ if biologically absent elements are encapsulated. Here we show that sealed single-walled CNTs filled with lead, barium and even krypton can be produced, and externally decorated with peptides to provide affinity for sub-cellular targets. The agents are able to highlight specific organelles in multiplexed XRF mapping, and are, in principle, a general and versatile tool for this, and other modes of biological imaging

Fast and efficient QTL mapper for thousands of molecular phenotypes

In order to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq require methods that rapidly correlate tens of thousands of molecular phenotypes with millions of genetic variants while appropriately controlling for multiple testing

Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction.

Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction