Advancing Fusion with Machine Learning Research Needs Workshop Report

Machine learning and artificial intelligence (ML/AI) methods have been used successfully in recent years to solve problems in many areas, including image recognition, unsupervised and supervised classification, game-playing, system identification and prediction, and autonomous vehicle control. Data-driven machine learning methods have also been applied to fusion energy research for over 2 decades, including significant advances in the areas of disruption prediction, surrogate model generation, and experimental planning. The advent of powerful and dedicated computers specialized for large-scale parallel computation, as well as advances in statistical inference algorithms, have greatly enhanced the capabilities of these computational approaches to extract scientific knowledge and bridge gaps between theoretical models and practical implementations. Large-scale commercial success of various ML/AI applications in recent years, including robotics, industrial processes, online image recognition, financial system prediction, and autonomous vehicles, have further demonstrated the potential for data-driven methods to produce dramatic transformations in many fields. These advances, along with the urgency of need to bridge key gaps in knowledge for design and operation of reactors such as ITER, have driven planned expansion of efforts in ML/AI within the US government and around the world. The Department of Energy (DOE) Office of Science programs in Fusion Energy Sciences (FES) and Advanced Scientific Computing Research (ASCR) have organized several activities to identify best strategies and approaches for applying ML/AI methods to fusion energy research. This paper describes the results of a joint FES/ASCR DOE-sponsored Research Needs Workshop on Advancing Fusion with Machine Learning, held April 30–May 2, 2019, in Gaithersburg, MD (full report available at https://science.osti.gov/-/media/fes/pdf/workshop-reports/FES_ASCR_Machine_Learning_Report.pdf). The workshop drew on broad representation from both FES and ASCR scientific communities, and identified seven Priority Research Opportunities (PRO’s) with high potential for advancing fusion energy. In addition to the PRO topics themselves, the workshop identified research guidelines to maximize the effectiveness of ML/AI methods in fusion energy science, which include focusing on uncertainty quantification, methods for quantifying regions of validity of models and algorithms, and applying highly integrated teams of ML/AI mathematicians, computer scientists, and fusion energy scientists with domain expertise in the relevant areas.

Cultivation of auricular chondrocytes in poly(ethylene glycol)/poly(ε-caprolactone) hydrogel for tracheal cartilage tissue engineering in a rabbit model

Tissue engineering has the potential to overcome the limitations of tracheal reconstruction. To tissue-engineer a tracheal cartilage, auricular chondrocytes were encapsulated in a photocurable poly(ethylene glycol)/poly(ε-caprolactone) (PEG/PCL) hydrogel. Chondrogenic genes, including Sox9, Acan and Col2a1, were up-regulated in auricular chondrocytes after 2 weeks of in vitro cultivation in the PEG/PCL hydrogel. Co-cultivation of 70 % auricular chondrocytes and 30 % bone marrow mesenchymal stem cells (BMSCs) accelerated the chondrogenic genes' expression in the PEG/PCL hydrogel. Cartilaginous matrix markers, including proteoglycans and collagen type II, were detected in the chondrocytes-encapsulated PEG/PCL hydrogel after 4 weeks of in vitro cultivation. The higher expression level of cartilaginous matrix markers was observed in the PEG/PCL hydrogel with co-cultivation of 70 % chondrocytes and 30 % BMSCs. After 4 weeks of ectopic cultivation in rabbits, the cylindrical PEG/PCL structure was sustained with the use of a luminal silicon stent. However, without the stent, the construct collapsed under a compression force. No fibrosis or vessel ingrowth were found in the PEG/PCL hydrogel after 4 weeks of ectopic cultivation, whereas the auricular chondrocytes showed proteoglycans' accumulation and collagen type II production. Rabbit auricular chondrocytes could survive and retain chondrogenic ability in the PEG/PCL hydrogel under both in vitro and in vivo conditions. While the PEG/PCL hydrogel did not show sufficient mechanical properties for supporting the cylindrical shape of the construct, the high chondrogenesis level of chondrocytes in the PEG/PCL hydrogel displayed the potential of this material for tracheal tissue engineering.

Traumatic Dissections of Bilateral Internal carotid Artery with Aneurysms Formation

Carotid artery dissection is an unusual complication of blunt neck trauma with high mortality and severe neurological deficits. Traumatic bilateral dissections and dissecting aneurysms are extremely rare. A 17-year-old male presented to our emergency department with sudden onset of right hemiparesis and aphasia. Initial computed tomography scan of head and neck showed no remarkable finding. On the second day, a magnetic resonance angiography of head and neck demonstrated bilateral extracranial internal carotid artery dissections. The diagnosis of traumatic carotid artery dissection for emergency physicians is difficult because of the absence or delayed onset in symptomatology. Magnetic resonance angiography is currently considered as an appropriate initial diagnostic tool for carotid artery injury. In clinical practice, early diagnosis by keeping a high index of suspicions is required by emergency physicians.

Increased risk of hepatitis B virus reactivation in systemic lupus erythematosus patients receiving immunosuppressants: a retrospective cohort study

Objective We aimed to investigate risk of hepatitis B virus reactivation in systemic lupus erythematosus patients with different hepatitis B virus infection statuses receiving immunosuppressive therapy. Methods We retrospectively analyzed systemic lupus erythematosus patients with positive hepatitis B surface antigen or anti-hepatitis B core IgG antibody who underwent immunosuppressive therapies from January 2001 to December 2012 at a medical center in Taiwan for evidence of hepatitis B virus reactivation. Results During this period, 906 out of 3125 patients who were diagnosed with systemic lupus erythematosus received screening tests for hepatitis B virus. Thirty-eight patients were identified as hepatitis B surface antigen-positive. Fifteen of 38 (39.5%) hepatitis B surface antigen-positive patients developed hepatitis B virus reactivation, and 53.3% of these patients experienced severe hepatitis flare. Three of 157 hepatitis B surface antigen-negative/anti-hepatitis B core IgG antibody-positive patients (1.9%) experienced hepatitis B surface antigen seroreversion after immunosuppressive therapy. Five patients received prophylactic or preemptive antiviral therapy and none of them developed hepatitis B virus flares. A daily dose of prednisolone greater than 5 mg was a risk factor for hepatitis B reactivation by multivariate logistic analysis. Conclusions The risk of hepatitis B virus reactivation is high in lupus patients receiving immunosuppressive therapy. Antiviral prophylaxis or preemption can effectively reduce the incidence of hepatitis B virus reactivation in lupus patients.

Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons analogous to Chen and Parker [Phys. Plasmas 8, 441 (2001)]. Two representative long wavelength modes, shear Alfvén waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries.

Fast Low-to-High Confinement Mode Bifurcation Dynamics in a Tokamak Edge Plasma Gyrokinetic Simulation

Transport barrier formation and its relation to sheared flows in fluids and plasmas are of fundamental interest in various natural and laboratory observations and of critical importance in achieving an economical energy production in a magnetic fusion device. Here we report the first observation of an edge transport barrier formation event in an electrostatic gyrokinetic simulation carried out in a realistic diverted tokamak edge geometry under strong forcing by a high rate of heat deposition. The results show that turbulent Reynolds-stress-driven sheared E×B flows act in concert with neoclassical orbit loss to quench turbulent transport and form a transport barrier just inside the last closed magnetic flux surface.

Additional chromosomal abnormalities in core-binding factor acute myeloid leukemia

Despite sharing a similar genetic abnormality, patients with core binding factor acute myeloid leukemia (CBF-AML), which is characterized by the presence of t(8;21) or inv(16)/t(16;16), show heterogeneous survival. Other molecular or cytogenetic factors are supposed to have an impact on the prognosis. We enrolled 24 CBF-AML patients to determine the impact of cytogenetic abnormality, and c-KIT, FLT3, NPM1, and CEBPA mutations on the prognosis. Only three patients had the c-KIT mutation (3/24, 12.5%) and one had the FLT3 mutation. However, over half of the patients (14/24) harbored additional cytogenetic changes, including ten with loss of sexual chromosomes (LOS) [all in the t(8;21) group], and six had additional abnormalities (two cases had both LOS and additional abnormalities). From this small-number study, no association was found between c-KIT mutation and survival and relapse rate. However, additional chromosome abnormalities had a significant association with relapse of the disease (P = 0.027). Stem cell transplant had a trend of benefitting patients after relapse (P = 0.065). This implies that chromosome abnormalities occur in CBF-AML and might take part in the heterogeneous nature of CBF-AML.

Prognostic implication of molecular aberrations in cytogenetically normal acute myeloid leukemia patients receiving allogeneic hematopoietic stem cell transplantation

Different molecular aberrations can be discriminated into certain prognostic subgroups in cytogenetically normal acute myeloid leukemia (CN-AML) patients but their impact on allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains controversial and studies from Asian populations are lacking. Forty-two adult non-M3 AML patients receiving allo-HSCT from 2002 to 2009 in southern Taiwan were retrospectively reviewed for survey, 23 (54.7%) of whom were CN-AML. NPM1, FLT3-ITD, and CEBPA were analyzed. After a median follow-up of 104 weeks (range, 8 to 384), patients in the good risk group (harboring either NPM1 or CEBPA mutation without concurrent FLT3-ITD) showed a borderline worse overall survival (OS) compared with the intermediate/poor risk group (P = 0.08). Interestingly, a poorer OS was found in patients with the CEBPA mutation (P = 0.003) but not the NPM1 mutation (P = 0.96). No OS difference was found between patients with or without FLT3-ITD (P = 0.15). In patients receiving allo-HSCT at first remission, there was no significant OS benefit in the good risk group (P = 0.33). In patients receiving allo-HSCT beyond first remission, disease status played a major role (P = 0.006), irrespective of molecular aberrations. Allo-HSCT in good risk patients should be carefully evaluated in Taiwanese, especially in patients with the CEBPA mutation. Conversely, allo-HSCT should be considered in first remission in patients with an intermediate/poor risk, where it may overcome the adverse impact of FLT3-ITD. Disease status remained a main issue in patients receiving allo-HSCT beyond first remission.

Single domain m-plane ZnO grown on m-plane sapphire by radio frequency magnetron sputtering

High-quality m-plane orientated ZnO films have been successfully grown on m-plane sapphire by using radio frequency magnetron sputtering deposition. The introduction of a nanometer-thick, low-temperature-grown ZnO buffer layer effectively eliminates inclusions of other undesirable orientations. The structure characteristics of the ZnO epi-layers were thoroughly studied by synchrotron X-ray scattering and transmission electron microscopy (TEM). The in-plane epitaxial relationship between ZnO and sapphire follows (0002)(ZnO) [parallel] (112[overline]0)(sapphire) and (112[overline]0)(ZnO) [parallel] (0006)(sapphire) and the ZnO/sapphire interface structure can be described by the domain matching epitaxy along the [112[overline]0](ZnO) direction. The vibrational properties of the films were investigated by polarization dependent micro-Raman spectroscopy. Both XRD and micro-Raman results reveal that the obtained m-ZnO layers are under an anisotropic biaxial strain but still retains a hexagonal lattice.

Field-induced expansion deformation in Pb islands on Cu(111): evidence from energy shift of empty quantum-well states

We use scanning tunneling microscopy and spectroscopy to measure the energy shift of empty quantum-well (QW) states in Pb islands on the Cu(111) surface. It is found that, with an increase of the electric field, the behavior of the energy shift can be grouped into two different modes for most QW states. In the first mode, the state energy moves toward high energy monotonically. In the second mode, the state energy shifts to a lower energy initially and then turns around to a higher energy. Moreover, we have observed that the QW states of higher energy behave in preference to the first mode, but they gradually change to the second mode as the Pb island becomes thicker. This thickness-dependent behavior reflects the existence of local expansion in the Pb islands, due to the electric field, and that the expansion is larger for a thicker island. QW states can thus be used for studying the localized lattice deformation in the nanometer scale.

Mandible changes evaluated by computed tomography following Botulinum Toxin A injections in square-faced patients

BACKGROUND

A facial contour that is oval is more pleasing in Asian women. Patients with a square face often seek facial contouring procedures to improve their appearance. Treatment often involves various combinations of Botulinum NeuroToxin A (BoNTA) injections into the masseters and/or mandibular angle resection. Many physicians claim that muscle paralysis with injections alone will decrease pulling on the underlying bone and also treat underlying bony flaring when present. Muscular changes after BoNTA injections have been well documented. However, the effect of BoNTA injections on the underlying mandibular bone morphology has not been studied to the best of the authors' knowledge. The goal of this study was to determine whether there are mandibular changes after masseter injection with botulinum toxin.

METHODS

In this retrospective study of ten female patients seeking treatment for a square face, three-dimensional CT scans were taken before and 3 months after standardized BoNTA injections in bilateral masseters. Mandibular cortex thickness, mandibular bone thickness, and mandibular volume were measured.

RESULTS

Soft-tissue changes were observed but no bony changes were observed 3 months after injections.

CONCLUSIONS

In this study of adult patients, there were no statistically significant mandibular changes 3 months after BoNTA injection. The current theory of mandibular flaring resolution after partial muscle paralysis is not supported by our findings. Therefore, a patient presenting both masseteric hypertrophy and bony flaring will most likely require a combined muscular and bony procedure.

A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan

Molecular and phenotypic data have been combined to characterize the genetic diversity of six local chicken breeds maintained with a long-term conservation programme. Hua-Tung, Hsin-Yi, Ju-Chi and Quemoy originated from Taiwan, Shek-Ki is from South China, and Nagoya is from Japan. Molecular tools included 24 microsatellite markers, melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) (MC1R), the LEI0258 marker located within the major histocompatibility complex (MHC), and mitochondrial DNA. Performance was recorded on the same individuals for body weight, panting rate in summer and antibody response (antigens: Newcastle disease virus and sheep red blood cells). A multivariate method previously proposed for taxonomy was used to combine the different data sets. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) and the MCW330 marker contributed the most to the first axis of the multiple coinertia analysis of molecular markers. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) showed evidence of selection, probably related to its effect on feather colour. The MHC exhibited a large diversity, with 16 alleles of the LEI0258 marker. Immune response traits contributed the most to the principal component analysis of phenotypic data. Eight mitochondrial DNA haplotypes related to clades A, B, C and E were distributed across breeds and revealed an important contribution of Indian and European breeds to Ju-Chi, Quemoy and Hsin-Yi. Phenotypic data contributed less than molecular data to the combined analysis, and two markers, LEI0258 and LEI0228, contributed the most. The combined analysis could clearly discriminate all breeds, except Ju-Chi, which was similar to Quemoy for many criteria, except immune response.

Investigation of magnetic properties and microstructure of ultrathin Co films grown on Si(111)- 7 x 7 surface

Magnetic properties and growth mechanism of ultrathin Co films on Si(111)-7 x 7 surface have been studied by using both surface magneto-optic Kerr effect (SMOKE) and scanning tunneling microscopy (STM), respectively. STM results show that the growth mechanism of ultrathin Co films on Si(111)-7 x 7 surface at room temperature belongs to Stranski-Krastanov (SK) growth mode. Due to formation of CoSi2 layer, no magnetic signal could be detected by SMOKE for 1-4 ML Co deposited on Si(111) surface. Because of rougher surface, both longitudinal and perpendicular magnetic anisotropy configuration appear for 4.2-10 ML Co/Si(111) films. When the Co thickness is increased to 10 ML, only longitudinal anisotropy configuration is found, resulting from the contribution to the volume anisotropy. Furthermore, in-plane coercivity increases with Co coverage because of enhancement of ferromagnetic coupling with Co thickness, out-of-plane coercivity increases with Co coverage due to the increment of demagnetized field, induced by the rougher Co surface and pinhole structures.

Classical reflux symptoms, hiatus hernia and overweight independently predict pharyngeal acid exposure in patients with suspected reflux laryngitis

BACKGROUND

Gastro-oesophageal reflux disease (GERD) has been associated with reflux laryngitis.

AIMS

To investigate the risk factors and the predictors of pharyngeal acid reflux (PAR) in Taiwanese patients with suspected reflux laryngitis.

METHODS

With referral from ENT physicians, 104 patients with symptoms and signs suggestive of reflux laryngitis completed a validated symptom questionnaire, an upper endoscopy exam and ambulatory 24-h pH tests with three sensors located at the hypopharynx, proximal and distal oesophagus. Patients with one or more episodes of PAR were considered abnormal.

RESULTS

Pharyngeal acid reflux was identified in 17% (18/104) of patients. In multivariate logistic regression analysis, PAR was independently associated with classical reflux symptoms [adjusted odds ratio (aOR) = 3.5, 95% confidence interval (CI): 1.0-12.8], hiatus hernia (aOR = 6.7, 95% CI: 1.5-30.2) and overweight (aOR = 3.4, 95% CI: 1.0-11.0). In predicting PAR, classical reflux symptoms had a sensitivity of 78% and hiatus hernia had a specificity of 95%. With all three factors, the positive predictive value for PAR was 80%. Classical reflux symptoms included heartburn, chest pain, dyspepsia and acid regurgitation.

CONCLUSIONS

Classical reflux symptoms, hiatus hernia and overweight are independent risk factors that may predict pharyngeal acid reflux in patients with suspected reflux laryngitis.

On the validity of the local diffusive paradigm in turbulent plasma transport

A systematic, constructive and self-consistent procedure to quantify nonlocal, nondiffusive action at a distance in plasma turbulence is exposed and applied to turbulent heat fluxes computed from the state-of-the-art full- f, flux-driven gyrokinetic GYSELA and XGC1 codes. A striking commonality is found: heat transport below a dynamically selected mesoscale has the structure of a Lévy distribution, is strongly nonlocal, nondiffusive, scale-free, and avalanche mediated; at larger scales, we report the observation of a self-organized flow structure which we call the " E × B staircase" after its planetary analog.

Co nanoislands on Au(111) and Cu(111) surfaces studied by scanning tunneling microscopy and spectroscopy

Co nanoislands on the Au(111) and Cu(111) surfaces have been studied by scanning tunneling microscopy and spectroscopy. The experimental results showed that Co nanoislands prefer to aggregate at the step edge and dislocation sites on the reconstructed Au(111) surface and at the step edge on the Cu(111) surface, respectively. In addition, based on dZ/dV-V spectra, in both the Co/Au(111) and the Co/Cu(111) systems, Gundlach oscillation was observed. From the peak shift of dZ/dV-V spectra between Co nanoisland and substrate surface, we can quantitatively obtain that the constant energy separation is -0.13 +/- 0.01 eV for the Co/Au(111) system, and 0.41 +/- 0.02 eV for the Co/Cu(111) system, respectively. These values indicate the work function difference between Co nanoisland and these surfaces.

Varying postprandial abdominovagal and cardiovagal activity in normal subjects

BACKGROUND

Several studies have supported the hypothesis of different presentations in the autonomic nervous system (ANS) between cardiac and gastric vagal activity. Due to the regionality of the ANS, different responses among different organ systems to the same stimulation (such as a meal) are quite possible.

METHODS

In this study we monitored the postprandial changes of heart rate variability (HRV) and gastrointestinal (GI) hormones to determine whether both responded in a similar pattern. Twenty-two healthy volunteers (6 males and 16 females) were enrolled. After recording a baseline ECG rhythm, further recordings were made at 20 min intervals for 120 min after a test meal. Serum human pancreatic polypeptide (PP), leptin, and total and active ghrelin levels were measured.

KEY RESULTS

After the meal, HR increased significantly from baseline at each time point, except for 20 min after the meal. The high frequency (HF) power decreased significantly from 40 min to 120 min after the meal. In addition, the low frequency (LF) power also decreased significantly from 60 min to 120 min. However, the LF:HF ratio increased significantly from 20 min to 120 min. There was a marked increase (>2 fold) of PP at 20 min after the meal, and the increase was sustained throughout the test period.

CONCLUSIONS & INFERENCES

These findings suggest that HRV reflects cardiac, but not equivalently, abdominovagal activity. Therefore, HRV as an abdominovagal activity measurement in patients with GI functional problems should be used with caution, and other markers such as PP should be included.

IL-10 promoter gene polymorphisms and sustained response to combination therapy in Taiwanese chronic hepatitis C patients

BACKGROUND AND AIMS

Host genetic factors may affect clinical outcomes of hepatitis C virus (HCV) infection; however, the possible mechanisms remain largely unknown. The role of immunopathogenesis in chronic hepatitis C leads to extensive exploration of host immunity including inflammatory cytokines.

METHODS

We examined interleukin 10 (IL-10) promoter gene polymorphisms at positions -1082, -819, and -592 relative to transcription start site and studied their association with response to 24 weeks of pegylated interferon plus ribavirin treatment in 143 chronic hepatitis C patients, of whom 97 (67.8%) achieved a sustained virologic response (SVR). In addition, 134 healthy adults were used as controls.

RESULTS

Of chronic hepatitis C patients, 111 (77.6%) were genotype 1 infection, 32 (22.4%) were genotype 2 infection. Patients with sustained virologic response were younger and had higher pretreatment ALT levels than those without. No statistical difference was found between chronic hepatitis C patients who achieved SVR or not in terms of gender, HCV genotype, pretreatment HCV RNA levels, and severity of liver disease. The serum IL-10 levels were comparable between healthy controls and chronic hepatitis C patients as well as between HCV patients with and without SVR. The distribution of IL-10 promoter gene polymorphisms at positions -1082, -819, and -592 relative to transcription start site was comparable between HCV patients and healthy controls as well as HCV patients with and without SVR. A high frequency of ATA haplotype of common IL-10 promoter gene SNPs was found in both chronic hepatitis C patients (70.3%) and healthy controls (69.8%). However, ATA haplotype was not associated with SVR in chronic hepatitis C patients.

CONCLUSIONS

Our data fail to demonstrate the influence of IL-10 promoter gene polymorphisms on the response to combination therapy in Taiwanese chronic hepatitis C patients. The impact of genetic variations in IL-10 haplotype on the response to anti-HCV treatment among different ethnic populations deserves further examination.

Phase contribution of image potential on empty quantum well States in pb islands on the cu(111) surface

We use scanning tunneling spectroscopy to explore the quantum well states in the Pb islands grown on a Cu(111) surface. Our observation demonstrates that the empty quantum well states, whose energy levels lie beyond 1.2 eV above the Fermi level, are significantly affected by the image potential. As the quantum number increases, the energy separation between adjacent states is shrinking rather than widening, contrary to the prediction for a square potential well. By simply introducing a phase factor to reckon the effect of the image potential, the shrinking behavior of the energy separation can be reasonably explained with the phase accumulation model. The model also reveals that there exists a quantum regime above the Pb surface in which the image potential is vanished. Moreover, the quasi-image-potential state in the tunneling gap is quenched because of the existence of the quantum well states.

Manifestation of work function difference in high order Gundlach oscillation

Gundlach oscillation (or the standing-wave state) is a general phenomenon manifesting in the tunneling spectrum acquired from a metal surface using scanning tunneling spectroscopy. Previous studies relate the energy shift between peaks of the lowest-order Gundlach oscillation observed on the thin film and the metal substrate to the difference in their work functions. By observing Gundlach oscillations on Ag/Au(111), Ag/Cu(111), and Co/Cu(111) systems, we demonstrate that the work function difference is not the energy shift of the lowest order but the ones of higher order where a constant energy shift exhibits. Higher order Gundlach oscillations can thus be applied to determine the work function of thin metal films precisely.