Machine Science in Biomedicine: Practicalities, Pitfalls and Potential

Machine Science, or Data-driven Research, is a new and interesting scientific methodology that uses advanced computational techniques to identify, retrieve, classify and analyse data in order to generate hypotheses and develop models. In this paper we describe three recent biomedical Machine Science studies, and use these to assess the current state of the art with specific emphasis on data mining, data assessment, costs, limitations, skills and tool support

Ab initio parametrised model of strain-dependent solubility of H in alpha-iron

The calculated effects of interstitial hydrogen on the elastic properties of alpha-iron from our earlier work are used to describe the H interactions with homogeneous strain fields using ab initio methods. In particular we calculate the H solublility in Fe subject to hydrostatic, uniaxial, and shear strain. For comparison, these interactions are parametrised successfully using a simple model with parameters entirely derived from ab initio methods. The results are used to predict the solubility of H in spatially-varying elastic strain fields, representative of realistic dislocations outside their core. We find a strong directional dependence of the H-dislocation interaction, leading to strong attraction of H by the axial strain components of edge dislocations and by screw dislocations oriented along the critical slip direction. We further find a H concentration enhancement around dislocation cores, consistent with experimental observations.Comment: part 2/2 from splitting of 1009.3784 (first part was 1102.0187), minor changes from previous version

Chandra Observations of the Crab-like Supernova Remnant G21.5-0.9

Chandra observations of the Crab-like supernova remnant G21.5-0.9 reveal a compact central core and spectral variations indicative of synchrotron burn-off of higher energy electrons in the inner nebula. The central core is slightly extended, perhaps indicating the presence of an inner wind-shock nebula surrounding the pulsar. No pulsations are observed from the central region, yielding an upper limit of ~40% for the pulsed fraction. A faint outer shell may be the first evidence of the expanding ejecta and blast wave formed in the initial explosion, indicating a composite nature for G21.5-0.9.Comment: 4 pages, 2 figures, formatted with emulateapj, submitted to ApJ

Adiabatic and Non-Adiabatic Contributions to the Free Energy from the Electron-Phonon Interaction for Na, K, Al, and Pb

We calculate the adiabatic contributions to the free energy due to the electron--phonon interaction at intermediate temperatures, $0 \leqslant k_{B} T < \epsilon_{F}$ for the elemental metals Na, K, Al, and Pb. Using our previously published results for the nonadiabatic contributions we show that the adiabatic contribution, which is proportional to $T^{2}$ at low temperatures and goes as $T^{3}$ at high temperatures, dominates the nonadiabatic contribution for temperatures above a cross--over temperature, $T_{c}$, which is between 0.5 and 0.8 $T_{m}$, where $T_{m}$ is the melting temperature of the metal. The nonadiabatic contribution falls as $T^{-1}$ for temperatures roughly above the average phonon frequency.Comment: Updated versio

On Zurek's derivation of the Born rule

Recently, W. H. Zurek presented a novel derivation of the Born rule based on a mechanism termed environment-assisted invariance, or "envariance" [W. H. Zurek, Phys. Rev. Lett. 90(2), 120404 (2003)]. We review this approach and identify fundamental assumptions that have implicitly entered into it, emphasizing issues that any such derivation is likely to face.Comment: 8 pages; v2: minor clarifications added; v3: reference to Zurek's quant-ph/0405161 added. To appear in Foundations of Physics (Cushing Volume

Nucleon, Δ\Delta and Ω\Omega excited states in Nf=2+1N_f=2+1 lattice QCD

The energies of the excited states of the Nucleon, $\Delta$ and $\Omega$ are computed in lattice QCD, using two light quarks and one strange quark on anisotropic lattices. The calculation is performed at three values of the light quark mass, corresponding to pion masses $m_{\pi}$ = 392(4), 438(3) and 521(3) MeV. We employ the variational method with a large basis of interpolating operators enabling six energies in each irreducible representation of the lattice to be distinguished clearly. We compare our calculation with the low-lying experimental spectrum, with which we find reasonable agreement in the pattern of states. The need to include operators that couple to the expected multi-hadron states in the spectrum is clearly identified.Comment: Revised for publication. References added, Table VI expanded to add strange baryon multiparticle thresholds and multiparticle thresholds added to Figs. 4, 5 and 6. 15 pages, 6 figure

A predictive model of the effect of therapeutic radiation on the human ovary

Radiation to the female pelvis as part of treatment for cancer predisposes young women to develop Premature Ovarian Insufficiency (POI). As the human female is born with their full complement of non-growing follicles which decline in an exponential fashion until the menopause, the age at which POI occurs is dependent on the age of the patient at treatment and the dose received by the ovary. A model that predicts the age at which POI occurs for a known dose at a known age will aid counselling patients on their fertility risk. Patients deemed to be at high risk of POI may be considered to be good candidates for established fertility preservation techniques. An updated and externally validated model of the age-related decline in human ovarian reserve was combined with the best available estimate of the median lethal dose LD for the human ovary. Using known age at diagnosis and posited radiotherapy treatment plan to estimate the dose to the least-affected ovary, we use an age-related model of the decline in ovarian reserve to generate a personalized age prediction of premature ovarian insufficiency. Our algorithm is available as an online calculator which graphs model outputs to inform discussions around survivor fertility. We report four example cases across different ages and diagnoses, each with two carefully designed photon and proton treatment plans. The treatment options are compared in terms of remaining fertile lifespan for the survivor. International oncology guidelines now mandate the consideration of later fertility when reviewing treatment options for children diagnosed with cancer. Our calculator (https://sites.cs.st-andrews.ac.uk/radiosensitivity), and the underlying algorithm and models, allow detailed predictions of the impact of various radiotherapy plans on fertility. These patient-specific data enhance pre-treatment discussions around post-treatment fertility and fertility preservation.Publisher PDFPeer reviewe

Millimeter wave satellite concepts. Volume 1: Executive summary

The objectives of the program were: (1) development of methodology based on the technical requirements of potential services that might be assigned to millimeter wave bands for identifying the viable and appropriate technologies for future NASA millimeter research and development programs, and (2) testing of this methodology with user applications and services. The scope of the program included the entire communications network, both ground and space subsystems. The reports include: (1) cost, weight, and performance models for the subsystems, (2) conceptual design for point-to-point and broadcast communications satellites, (3) analytic relationships between subsystem parameters and an overall link performance, (4) baseline conceptual systems, (5) sensitivity studies, (6) model adjustment analyses, (7) identification of critical technologies and their risks, (8) brief R&D program scenarios for the technologies judged to be moderate or extensive risks

Long-term follow up to assess criteria for ovarian tissue cryopreservation for fertility preservation in young women and girls with cancer

Funding: K.D. is supported by a CRUK grant (C157/A25193). This work was undertaken in part in the MRC Centre for Reproductive Health, (supported by MRC grant MR/N022556/1). R.A.A. has received consulting fees from Ferring and Roche Diagnostics; payment from Merck and IBSA for educational events; and laboratory materials from Roche Diagnostics.STUDY QUESTION Do the Edinburgh Selection Criteria correctly identify female cancer patients under the age of 18 who are at risk of premature ovarian insufficiency (POI) as candidates for ovarian tissue cryopreservation (OTC)? SUMMARY ANSWER Patient assessment using these criteria accurately identifies those at risk of POI, who can be offered OTC and future transplantation as a means of fertility preservation. WHAT IS KNOWN ALREADY Treatment for childhood cancer can have adverse consequences on future fertility; at the time of diagnosis, fertility risk assessment should be undertaken in order to identify patients to whom fertility preservation should be offered. The Edinburgh selection criteria, based on planned cancer treatment and patient health status, are utilized to identify those at high risk and therefore eligible for OTC. However, this procedure is not without risk and there are few data on the efficacy of the procedure in prepubertal patients. As such, long-term follow-up of reproductive outcomes is necessary, to ensure that OTC is being offered appropriately. STUDY DESIGN, SIZE, DURATION Cohort study encompassing all females diagnosed with cancer under the age of 18 in South East Scotland, from 1 January 1996 to 30 April 2020. Patients were followed up for reproductive outcomes to assess for diagnosis of POI. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 638 eligible patients were identified; patients under the age of 12 or deceased before the age of 12 were excluded from the study, leaving a study population of 431 patients. Electronic records were reviewed for reproductive function, assessed by current menstruation, pregnancy (in the absence of POI diagnosis), reproductive hormone measurements, pubertal progression, or diagnosis of POI. Patients on hormonal contraception (other than for treatment of POI or panhypopituitarism with no history of gonadatoxic treatment) were excluded from analysis (n = 9). Analysis on remaining 422 patients was carried out using the Kaplan–Meier methods, with POI as the defined event, and Cox proportional hazards model. MAIN RESULTS AND THE ROLE OF CHANCE In the study population of 431 patients, median ages at diagnosis and analysis were 9.8 and 22.2 years, respectively. Reproductive outcomes were unavailable in 142 patients; the assumption was made that these patients did not have POI, but a subanalysis excluding these patients was also performed. Of the 422 patients aged >12 at analysis and not taking hormonal contraception, OTC was offered to 37 patients and successfully performed in 25 patients. Of the 37 patients offered OTC (one at time of relapse), nine (24.3%) developed POI. Of the 386 not offered OTC, 11 (2.9%) developed POI. The probability of developing POI was significantly higher in those offered OTC (hazard ratio [HR] 8.7 [95% CI 3.6–21]; P < 0.0001), even when those patients with unknown outcomes were excluded from the analysis (HR 8.1 [95% CI 3.4–20]; P < 0.001). All patients offered OTC who developed POI did so after treatment for primary disease; in those not offered OTC, five patients (45.5%) developed POI after treatment for disease relapse. LIMITATIONS, REASONS FOR CAUTION A significant number of patients had unknown reproductive outcomes; many of these patients were engaged in ongoing follow-up but did not have documented reproductive assessment. This may have introduced bias to the analysis and highlights the need for reproductive follow-up as part of routine cancer aftercare. In addition, the relatively young age of the patient population and short duration of follow-up in some cases demonstrates the need for ongoing follow-up of this cohort. WIDER IMPLICATIONS OF THE FINDINGS The prevalence of POI after childhood cancer is low, but the Edinburgh selection criteria remain a robust tool for selecting those at high risk at the time of diagnosis, to offer OTC appropriately. However, disease relapse necessitating more intensive treatments remains a challenge. This study additionally highlights the importance of routine assessment and documentation of reproductive status in haematology/oncology follow-up.Publisher PDFPeer reviewe