Overall Survival Prediction in Stereotactic Radiosurgery Patients with Glioblastoma Via a Deep-Learning Approach

PURPOSE/OBJECTIVE(S)

Accurate and automated early survival prediction is critical for glioblastoma (GBM) patients as their poor prognosis requires timely treatment decision-making. We have developed a deep learning (DL)-based GBM overall survival (OS) prediction model based on a multi-institutional public dataset using only pre-operative basic structural multi-parametric magnetic resonance images (MRIs). The purpose of this study is to evaluate this DL-based OS prediction model with an institutional stereotactic radiosurgery (SRS) clinical trial dataset.

MATERIALS/METHODS

The task of this study is to classify GBM patients into 3 OS classes: long-survivors (>15 months), mid-survivors (between 10 and 15 months) and short-survivors (< 10 months). The proposed OS prediction model is an ensemble of a ResNet-based classifier and a K-NN classifier. The ResNet-based classifier is trained in a Siamese fashion to explore inter-class differences. During testing, training sample features are implemented with a K-NN classifier to ensemble with the ResNet-based classifier. A public dataset from Medical Image Computing and Computer Assisted Intervention (MICCAI) Brain Tumor Segmentation (BraTS) challenge 2020 (235 patients) were used for model establishing and initial validation. Then the validated model was evaluated on 19 GBM patients from an institutional SRS clinical trial. Each data entry consists of pre-operative basic structural multi-parametric MRIs and survival days, as well as patient ages for BraTS data and basic clinical characteristics for institutional data. GBM sub-regions, including contrast-enhancing tumor, peri-tumoral edema, and necrotic/non-enhancing tumor core, were segmented in the multi-parametric MRIs by an in-house DL model for both datasets. The OS prediction model was trained on 90% of the segmented BraTS data and validated on the rest 10%, then further evaluated on the institutional data. The model performance was assessed by prediction accuracy (ACC) and the area under the curve (AUC).

RESULTS

For this 3-class OS classification task, our DL-based prediction model achieved an ACC of 65.22% and an AUC of 0.81 on the BraTS dataset compared with the top-ranked result from the BraTS challenge 2020 (Rank 1st: ACC 61.7%), and an ACC of 52.63% and an AUC of 0.69 on the institutional dataset. Further analysis of the institutional dataset found that the predicted OS class had a statistically significant correlation with treatment volume (p = 0.012) and age (p = 0.006), which matches the analysis that the patients' ground truth OS class is statistical significantly correlated with treatment volume (p = 0.045).

CONCLUSION

Our DL-based OS prediction model for GBM using basic structural multi-parametric pre-operative MRIs has demonstrated promising performance in both public and institutional dataset with minimal manual processing requirements. This OS prediction model can be potentially applied to assist timely clinical decision-making.

Sudden-Discharging Quench Dynamics in a No-Insulation Superconducting Coil

It is generally agreed that no-insulation (NI) high-temperature superconducting (HTS) magnets do not quench because of the turn-to-turn energy-releasing bypass unique to NI. However, these magnets, especially with high operating current and low ambient thermal capacity, still occur unexpected quenches when the current through the magnets suddenly drops to zero (i.e., the sudden-discharging quench). Here, we report this kind of quench, which is different from that widely-reported quench happening during charging (i.e., the energizing quench). Here, a demonstrative coil with 655-turns, 350 A operating current, and 4 K conduction cooling, is used to prove this sudden-discharging quench, and a simulation model is built to reveal the quench dynamics. Results show the turn-to-turn heat triggers the initial partial quench in the inner coil turns and then the induced overcurrent spreads out the quench like an avalanche to the outer coil turns.

Conceptual Design of a Portable, Solid-Nitrogen-Cooled 0.5-T/560-mm Point-of-Care MRI Magnet

We describe the conceptual design of a portable, liquid-helium-free, all-REBCO, 0.5-T/560-mm point-of-care magnetic resonance imaging (MRI) magnet. It is free from an external power supply and a refrigeration system during operation. In our portable MRI magnet, we use a detachable "cryocirculator" that circulates, in a closed circuit, cold working fluid, and most importantly for portability, it can be readily coupled to or decoupled from the magnet, in contrast, a conventional cryocooler is mechanically attached to the magnet. Another unique feature of our system is a volume of solid nitrogen (SN2) in the cold chamber that adds enough thermal mass to the magnet in the 30-36-K operating temperature range, enabling it to maintain its field over a period of, for this system, ≥10 hours, plenty enough for this portable MRI system, uncoupled from its cryocirculator, to perform its mission before it needs recooling.

First-Cut Design of a Benchtop Cryogen-Free 23.5-T/25-mm Magnet for 1-GHz Microcoil NMR

As a preliminary work, we have completed a 12.5-mm-cold-bore high-temperature superconducting (HTS) REBCO magnet prototype and successfully operated it up to 25 T at 10 K cooled by a cryocooler only, without liquid helium. In this paper we present the first-cut design of a cryogen-free all-REBCO 23.5-T/25-mm-warm-bore magnet having a high homogeneity of <0.1 ppm over a 1-cm diameter of spherical volume for a benchtop 1-GHz microcoil NMR spectroscopy. We also investigate a shielding design to reduce a 5-gauss fringe field radius to ≤1.5 m. This benchtop magnet will incorporate all the innovative design and operation concepts validated by the prototype magnet: 1) all-HTS composition and operation at above 4.2 K; 2) no-insulation winding technique with an extra shunting that makes this high-field REBCO magnet compact, mechanically robust, and self-protecting; 3) a single coil formation that leads, compared with the traditional multi-nested high-field NMR magnet, to simpler and more affordable manufacturing processes; 4) operational temperature-controlled screening-current reduction method which reduces peak stresses within the REBCO coil and field errors; and 5) cryogenic design for conduction-cooling operation.

Self-Protection Characteristic Comparison between No-Insulation, Metal-as-Insulation, and Surface-Shunted-Metal-as-Insulation REBCO coils

The metal tape co-winding or a metal-as-insulation (MI) winding method is an excellent way to improve the mechanical properties and reduce the average current density, thereby decreasing the stress in high-field REBCO magnet without completely losing the benefits of the no-insulation (NI) winding method. However, the MI winding increases the resistance between turns, which is known as characteristic resistance. The increased characteristic resistance can reduce the bypass current during abnormal transition situation, such as quench, which may not be desirable from a magnet protection point of view. To take advantage of both the MI and NI winding, one possible solution to reduce characteristic resistance of the MI winding coils is to add a shunt on top of the winding surface of the coil. We call this method surface-shunted-metal-as-insulation (SSMI). In this presentation, we compare the characteristic resistances and their correlated self-protecting characteristics between NI, MI, and SSMI. We present the test results of single pancake coils which wound using different winding methods (NI, MI, and SSMI) with same winding pressure of 20 N. In particular, we investigated how the SSMI method affects the characteristic resistance.

Magnetic Susceptibility of Andreev Bound States in Superfluid ^{3}He-B

Nuclear magnetic resonance measurements of the magnetic susceptibility of superfluid ^{3}He imbibed in anisotropic aerogel reveal anomalous behavior at low temperatures. Although the frequency shift clearly identifies a low-temperature phase as the B phase, the magnetic susceptibility does not display the expected decrease associated with the formation of the opposite-spin Cooper pairs. This susceptibility anomaly appears to be the predicted high-field behavior corresponding to the Ising-like magnetic character of surface Andreev bound states within the planar aerogel structures.

Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability

Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.

Review on Progresses and Challenges of Key Mechanical Issues in High-Field Superconducting Magnets

The development of modern science and technology requires high magnetic fields exceeding 25T. Second-generation high-temperature superconducting wires, i.e. REBCO (RE refers to Y, Gd, Dy, Eu and other rare earth elements) coated conductors (CCs), have become the first choice for the high-field magnet construction because of their high irreversible magnetic field. The mechanical stresses caused by manufacturing, thermal mismatch and Lorenz forces closely influence electromagnetic performance during operation for REBCO CCs, in addition, the recently concerned screen currents have effects on the mechanical characteristics of the high-field REBCO magnets. In this review, the experimental and main theoretical works of critical current degradation, delamination, fatigue and shear investigations on REBCO CCs are reviewed at first. Then, the research progress of screening current effect in the development of high-field superconducting magnets are introduced. Finally, the key mechanical problems in the future development of high-field magnets based on REBCO CCs are prospected.

On fault-mode phenomenon in no-insulation superconducting magnets: A preventive approach

Here, we present experimental and analytical results of a preventive approach applied to a fault-mode phenomenon caused by electrodes or power-source failure in a no-insulation (NI) high-temperature superconducting REBa2Cu3O7-x (REBCO, RE = rare earth) magnet. It is generally agreed that the NI magnets, at least those of laboratory scale, are self-protected from overheating and, therefore, from quenching, chiefly because of turn-to-turn current bypassing unique to NI. However, these NI magnets do experience unexpected quenches, e.g., when the current through the magnet suddenly drops due to the aforementioned fault-mode phenomenon. Here, we report this phenomenon of a sudden-discharging-triggered quench of an NI REBCO coil, conduction-cooled, and operated at 4.2 K. We also present our preventive approach for this phenomenon that relies on an appropriately designed resistor shunted across the coil terminals. With this shunt resistor, a quench was prevented by suppressing the quench initiating turn-to-turn heat and induced overcurrent within the NI winding, and the coil current decayed safely.

Injectable carbon nanotube-functionalized hydrogel as a tool for cardiac tissue engineering

Background/Introduction

Heart failure (HF) is an expensive major public health problem in the United States and around the world (1). The current treatments for HF are aimed at reducing symptoms, slowing disease progression, and reducing mortality and not aimed at repairing heart muscle or restoring function. Furthermore, even with these treatments, approximately half of patients with HF will die within 5 years of diagnosis (2). Cardiac transplantation remains the only definitive treatment for those affected with end-stage HF, but availability of donor hearts remains a major limitation (3).

Purpose

The ability of the adult heart to regenerate cardiomyocytes (CMs) lost after injury is limited, generating interest in developing tissue engineering therapies to avoid progression towards HF. Rigid carbon nanotubes (CNTs) scaffolds have been used to improve CMs viability, proliferation, and maturation (4), but require undesirable invasive surgeries for implantation. To overcome this limitation, we engineered an injectable reverse thermal gel (RTG) functionalized with CNTs (RTG-CNT) that transitions from a liquid-solution to a gel-based matrix shortly after reaching body temperature allowing for a liquid-based delivery rapidly followed by a stable-gel localization (5).

Methods and results

Here we show experimental evidences the RTG-CNT hydrogel, used as a three-dimensional (3D) niche to culture human induced pluripotent stem cells (hiPSC)-CMs, promotes hiPSC-CMs alignment and elongation with increased Cx43 localization and improved contraction function when compared with traditional two-dimensional (2D) fibronectin controls and plain 3D RTG system without CNTs. Moreover, the short-term (4-week) biocompatibility of the RTG-CNT hydrogel was also assessed in a mouse model (intracardial injection). The results confirmed that the RTG-CNT hydrogel is well tolerated by the cardiac tissue.

Conclusion

Our results indicated that the injectable RTG-CNT hydrogel has the potential to be used as a minimally invasive tool for cardiac tissue engineering efforts.

Funding Acknowledgement

Type of funding sources: Other. Main funding source(s): NATIONAL HEART, LUNG, AND BLOOD (NHLBI) INSTITUTE

Partial-Insulation HTS Magnet for Reduction of Quench-Induced Peak Currents

The No-insulation-like (NI) coil's turn-to-turn current paths prevent local heating by forcing the current to bypass into nearby turns when a hot spot appears in a coil. However, the changing direction of the current by bypassing will change the magnetic flux, which generates unwanted induced currents in the adjacent coils in a multiply-stacked HTS magnet. This induced current can temporarily exceed the designed maximum currents in the NI coils, damaging the magnet. A partial-insulation (PI) coil, in which a single or multiple insulated, with a polyimide-like material or a thin ceramic film, is inserted between windings to hinder the current paths, can reduce the peak induced currents in the NI HTS coil's current paths. In this paper, we present the results of a simulation study on the peak-induced current upon a quench of the PI HTS magnet with a double pancake. The study shows that the peak-induced current varies with the number of insulated turns. We also discuss the induced current turn-by-turn simulation. According to the simulation result, the PI effectively reduces overall induced current, especially insulation applied every two turns.

A Cryogen-Free 25-T REBCO Magnet with the Extreme-No-Insulation Winding Technique

We present the operation result of a cryogen-free 23.5 T/φ12.5 mm-cold-bore magnet prototype composed of a stack of 12 no-insulation (NI) REBCO single pancake coils-ten middle coils of 6-mm wide and two end coils of 8-mm wide tape-forming 6 double pancake (DP) coils with inner joints. Each coil was wound with the tape having only 1-μm-thick copper layer on each side to overcome the conductor thickness uniformity issue and enhance the mechanical strength within the winding, and then, additional electrical shunting by thin layers of solder was applied on the top and bottom surfaces of each DP coil for effective cooling and quench protection-called extreme-NI winding technique. With this small prototype magnet towards a benchtop 1-GHz NMR, we validate our coil design that include conductor performance, screening-current-induced field and stresses, and conduction-cooling cryogenics. Included in the paper are: 1) conductor issues and our counterproposal in winding; 2) screening-current reduction method; 3) design and manufacture summary of the magnet; and 4) operating test results of the magnet up to 25 Tesla.

Construction and test result of an all-REBCO conduction-cooled 23.5 T magnet prototype towards a benchtop 1 GHz NMR spectroscopy

A compact benchtop high-field REBCO NMR is one of the most promising HTS applications. An all-REBCO, conduction-cooled magnet is a very attractive design option for demonstrating the unique potential of REBCO for forefront magnets. In this research, we have successfully constructed and tested a prototype all-REBCO, conduction-cooled, 23.5 T magnet operating at 10 K. We have applied the concept of an extreme No-Insulation (NI) winding technique, coupled with a solder-shunting procedure to improve magnet performance. We have also used a temperature-controlled charging sequence (TCCS) to reduce the screening current. The magnet was energized to 23.6 T at 14 K; it was further operated to 25 T at 10 K for nearly 60 hours.

Dysregulation of immune cell and cytokine signaling correlates with clinical outcomes in myelodysplastic syndrome (MDS)

OBJECTIVES

Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis. Although hypomethylating agents (HMA) have improved survival in higher-risk MDS, most patients eventually succumb to progressive disease. Utilizing samples collected prospectively from three MDS clinical trials, we analyzed genetic and immunological biomarkers and correlated them with clinical outcomes.

METHODS

154 samples were analyzed from 133 de novo MDS patients for T-cell and myeloid cell immunophenotyping and gene expression analysis. Treatments were with HMA or immunomodulatory drug (IMiD) alone or in combination.

RESULTS

We observed differences in immune cell subsets between lower and higher risk IPSS groups with NKT cells, MDSCs, intermediate-proinflammatory and non-classical monocytes being higher in the latter group while naïve CD4+ T-cells were reduced. Intermediate-proinflammatory monocytes were increased in non-responders and those failing to achieve at least a hematological improvement. Pro-inflammatory NKT cells were increased at diagnosis for patients failing to derive clinical benefit after 12 months of treatment. Gene expression analysis of paired bone marrow (BM) colony-forming units (CFUs) from diagnosis and 4 cycles post-treatment confirmed that genes involved in cytokine signaling were downregulated in C4 normal colonies.

CONCLUSIONS

These findings support the central roles of dysregulation in innate immunity and inflammatory signaling in the pathogenesis of MDS which correlated with clinical outcomes post-treatment.

Design Overview of the MIT 1.3-GHz LTS/HTS NMR Magnet with a New REBCO Insert

We present a design overview of the MIT 1.3-GHz LTS/HTS NMR magnet (1.3G) with a newly designed 835-MHz REBCO insert (H835) as a replacement for the 800-MHz REBCO insert (H800) that was damaged when it quenched during operation in 2018. The new H835 is designed to contribute 19.6 T in a background field of 10.93 T by an LTS NMR magnet that normally rated at 11.74 T (500 MHz): combined, 1.3G generates a total field of 30.53 T corresponding to a proton resonance frequency of 1.3 GHz. H835 is designed to operate stably while meeting 1.3G design constraints. We have also designed H835 to protect it from permanent damage in an improbable event like a quench. Key design features are: 1) a single-coil formation, composed of 38 stacked metal-co-wound no-insulation and 2 stacked no-insulation double-pancake coils, all with mechanically improved cross-over sections; 2) enhanced thermal stability; and 3) reduced current margin with a detect-and-heat method. This paper includes: 1) electromagnetic and mechanical design of H835; 2) cryogenics overview; 3) quench protection strategy; and 3) discussion on the next steps to successfully complete 1.3G.

An MgB2 Superconducting Joint with its Own Heat-Treatment Schedule

We suggested an MgB₂ joint process with its own heat-treatment schedule to apply it for our 1.5-T MgB₂ "finger" MRI magnet. In fabricating the MgB₂ magnet, the optimal heat-treatment schedule to attain a reproducible and high critical current is different in a joint and a coil. To solve this problem, we introduced an additional heating system, which is composed of a cartridge heater and a thermocouple connected with a copper block, into a box-type furnace. Then, we carried out heat-treatments with exclusively increasing the joint-part temperature above the Mg melting point of 645 °C-the joint was actually heated up to 700 °C. We evaluated a critical current and a crystal structure of the obtained MgB₂ joint. From experimental results, we found that the joint heated with the own heat-treatment schedule, which is 700 °C for 1 h + 600 °C for 11 h, showed a good I _c of over 450 A at 15K under self-field. The joint resistance was estimated by the coil operation for 18 days, and it was expected to be less than 10^-12 Ω.

Hot-Spot Modeling of REBCO NI Pancake Coil: Analytical and Experimental Approaches

The No-Insulation (NI) winding provides intrinsic bypassing current paths that enable self-protection from overheating. The self-protection of the NI coil is one of the most promising protection techniques for the high field high-temperature superconductor (HTS) magnet applications. Since the additional paths are valid for an HTS magnet with a thinner matrix, the self-protection mechanism is applicable even for the higher current density magnet with reduced matrix thickness inside the HTS tape. However, reducing the matrix can cause damage to the magnet by producing excessive heat during the quench. This research introduces a new modeling method to investigate the hot-spot characteristics in the REBCO NI pancake coil. The model is also validated with a sample NI HTS coil experiment result. Radial direction Normal Zone Propagation (NZP) velocity of the sample coil is estimated based on the suggested model. The calculated radial direction NZP velocity is applied to calculate the center field drop of the NI HTS coil, and the result is well-matched with the experiment result. We also introduce one example of the model applications. The maximum current density that will not exceed a given reference temperature in the adiabatic cooling condition is estimated using the model.

Thyroid surgery during coronavirus-19 pandemic phases I, II and III: lessons learned in China, South Korea, Iran and Italy

OBJECTIVE

We compared demographic and clinic-pathological variables related to the number of surgeries for thyroid conditions or for cancer, morbidity, and fine needle aspiration (FNA) practices among Covid19 pandemic phases I, II, III and the same seasonal periods in 2019.

METHODS

The prospective database of the Division of Thyroid Surgery, China-Japan Union Hospital of Jilin University, Changchun, China was used for this study. Covid19 emergency levels were stratified according to the World Health Organization: phase I (January 25-February 25, 2020), phase II (February 26-March 19), phase III (March 20-April 20).

RESULTS

There were fewer outpatient FNAs and surgeries in 2020 than in 2019. There were no thyroid surgeries during phase I. There were also fewer surgeries for cancer with a significant reduction of advanced stage cancer treatments, mainly stage T1b N1a in phase II and T3bN1b in phase III. Operative times and postoperative stays were significantly shorter during the pandemic compared to our institutional baseline. In phase III, vocal cord paralysis (VCP) increased to 4.3% of our baseline numbers (P = 0.001). There were no cases of Covid19-related complications during the perioperative period. No patients required re-admission to the hospital.

CONCLUSION

The Covid19 outbreak reduced thyroid surgery patient volumes. The decrease of Covid19 emergency plans contributed to unexpected outcomes (reduction of early stage cancer treatment, decreased operative times and hospital stays, increased VCP rate).

Publisher Correction: Prototype REBCO Z1 and Z2 shim coils for ultra high-field high-temperature superconducting NMR magnets

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Identification of Pistacia-associated flexivirus 1, a putative mycovirus of the family Gammaflexiviridae, in the mastic tree (Pistacia lentiscus) transcriptome

In this study, we identified the genome sequence of the novel virus Pistacia-associated flexivirus 1 (PAFV1), a putative member of the mycovirus family Gammaflexiviridae (the order Tymovirales), via analysis of a transcriptome dataset for the mastic tree (Pistacia lentiscus, the family Anacardiaceae). PAFV1 was predicted to have three open reading frames (ORFs): ORF1, encoding a replicase (REP) with RNA-dependent RNA polymerase activity; ORF2, a movement protein (MP); and ORF3, a hypothetical protein. The PAFV1 REP sequence showed high similarity to those of three known members of the family Gammaflexiviridae i.e., Entoleuca gammaflexivirus 1 (EnFV1), Entoleuca gammaflexivirus 2 (EnFV2), and Botrytis virus F (BVF). A genome contig of the fungus Monosporascus cannonballus also contained a sequence of an endogenous virus similar to that of PAFV1. Sequence comparison and phylogenetic analysis indicated that PAFV1, EnFV1, and the endogenous virus of M. cannonballus formed a distinct subgroup (apart from EnFV2 and BVF), and may be the founding members of a novel genus in the family Gammaflexiviridae. Notably, MP sequences of PAFV1/EnFV1 showed similarity to the MP sequences of the mycovirus group called tobamo-like mycoviruses (an unassigned taxon), implying that genomic recombination occurred between members of the family Gammaflexiviridae and tobamo-like mycoviruses. Since PAFV1 is phylogenetically related to mycoviruses, PAFV1 may also be a mycovirus that infected a fungus associated with the mastic tree sample, which is evidenced by the presence of fungal ribosomal RNA sequences in the mastic tree transcriptome. Thus, the PAFV1 genome sequence may be useful in elucidating the genome evolution of Gammaflexiviridae and tobamo-like mycoviruses. Keywords: Pistacia-associated flexivirus 1; Gammaflexiviridae; mycovirus, mastic tree.

Clinical features of subungual melanoma according to the extent of Hutchinson's nail sign: a retrospective single-centre study

BACKGROUND

Hutchinson's nail sign (HS) is among the diagnostic criteria for subungual melanoma (SUM). However, there is minimal evidence supporting the overall clinical significance of HS in SUM.

OBJECTIVES

To identify clinicopathological features of SUM according to the extent of HS.

METHODS

Retrospective cohort study was performed with consecutive SUM patients at a single centre from January 2006 to December 2017. The extent of HS was defined by the number of affected nail folds (range 0-4). Comparison groups were organized as follows: patients with HS (affecting ≥1 nail folds) vs. without HS; patients with HS affecting ≥2 nail folds vs. HS affecting <2 nail folds; patients with HS affecting ≥3 nail folds vs. HS affecting <3 nail folds. Clinicopathological characteristics of SUM were compared between the groups.

RESULTS

Sixty-one SUM patients were included. Forty-six (75.4%) exhibited HS; 22 (47.8%) on a toe and 24 (52.2%) on a finger. In multivariate analysis, nail destruction [hazard ratio (HR), 10.00; 95% confidence interval (CI), 2.61-38.30; P = 0.001] was significantly associated with the presence of HS and amputation was significantly associated with HS affecting ≥2 nail folds (HR, 4.75; 95% CI, 1.36-16.61; P = 0.015). High T stage (HR, 1.85; 95% CI, 1.20-2.85; P = 0.005, Fig. 2) was significantly associated with HS appearing in ≥3 nail folds.

CONCLUSION

Besides its value of detecting SUM, HS provides useful clinical information. The number of nail folds exhibiting HS could be a useful clinical clue for planning therapeutic strategies for SUM.

TEK is a novel prognostic marker for clear cell renal cell carcinoma

OBJECTIVE

Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney cancer. However, effective therapeutics for ccRCC are lacking. Novel biomarkers could provide critical information when determining prognoses for patients with ccRCC. In this study, we sought to determine if the expression of receptor tyrosine kinase (TEK) could be a potential novel prognostic biomarker for ccRCC. TEK, originally identified as an endothelial cell-specific receptor, plays an important role in the modulation of vasculogenesis and remodeling. Altered TEK expression has been observed in tumor tissues (e.g., oral squamous cell carcinomas, leukemia) and breast, gastric and thyroid cancers. However, the role of TEK in ccRCC remains unknown.

PATIENTS AND METHODS

Differential TEK expression between non-metastatic (stage M0) and metastatic (stage M1) ccRCC patient cohorts was determined from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Furthermore, TEK expression was assessed as a prognostic factor using the time-dependent area under the curve (AUC) of Uno's C-index, the AUC value of the receiver operating characteristics (ROC) at 5 years, Kaplan-Meier survival curves and multivariate analyses.

RESULTS

A Kaplan-Meier curve analysis revealed that the downregulation of TEK expression was associated with a poor prognosis for patients with ccRCC with good discrimination (p<0.0001 and p=0.0044 for the TGCA and ICGC cohorts, respectively). Analyses of C-indices and receiver operating characteristic AUC values further support this discriminative ability. Moreover, multivariate analyses showed the prognostic significance of TEK expression levels (p<0.001).

CONCLUSIONS

Although additional clinical investigations will be needed, our results suggest that TEK is a potential biomarker for ccRCC.

Techniques for investigating mitochondrial gene expression

The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.

Experimental and Numerical Studies on a Method to Mitigate Screening Current-Induced Field for No-Insulation REBCO Coils

We present experimental and numerical studies on a method to mitigate screening current-induced field (SCF) for NI REBCO coil. The SCF is the major field error to incorporate a REBCO insert for a high field LTS/HTS magnet. The field-shaking technique is going to be used to mitigate the SCF of 800-MHz REBCO insert magnet (H800) for MIT 1.3-GHz LTS/HTS NMR magnet (1.3 G). The field-shaking using 500-MHz LTS background magnet generates the SCF in H800, due to huge self and mutual inductances of them. In this paper, we tested the effect of the induced current in the NI REBCO coil on the field-shaking technique to mitigate the SCF. The amount of the induced current was decided by the NI REBCO coil status; the open- or closed-loop coil. We performed the three cases of experimental tests and analyzed them. From the test results, we may conclude that we need to limit the ramp rate of L500 during the field-shaking, to minimize the induced current in the HTS insert which consists of the NI REBCO coil.

MIT 1.3-GHz LTS/HTS NMR Magnet: Post Quench Analysis and New 800-MHz Insert Design

We present post-quench analyses of the MIT 800-MHz REBCO insert magnet (H800), unexpectedly quenched during operation in March 2018, and design study of a new 800-MHz HTS insert (H800N). The as-wound H800 was supposed to contribute 18.7 T and, with an LTS background magnet (L500), produce 30.5 T corresponding to a proton resonance frequency of 1.3 GHz. The H800 was operated at 4.2 K in liquid helium and, about 5 minutes after the power supply reached a target operating current of 251.3 A, it experienced a quench. Because the damage in the H800 was more widespread than it first appeared, we decided to design and build a new insert magnet, H800N. In designing H800N, we try to eliminate unanticipated flaws in our H800 design. H800N is to be more stable not to quench and more reliably survive against quench without permanent damage by: 1) adopting a single solenoid structure composed of 40 stacked double pancake coils with improved cross-over sections; 2) enhancing thermal stability; and 3) reducing excessive current margin for quench protection.

A Tabletop Persistent-Mode, Liquid Helium-Free 1.5-T MgB2 "Finger" MRI Magnet: Construction and Operation of a Prototype Magnet

This paper presents results of construction and operation of a persistent-mode, liquid-helium-free, small-scale prototype magnet for the development of a tabletop 1.5-T "finger" MRI system for osteoporosis screening. The prototype magnet, composed of 2 MgB2 coils, one superconducting joint, and a persistent-current switch (PCS) built from a portion of one coil, was wound with a one continuous ~80-m long unreacted and monofilament MgB2 wire and then reacted. The test magnet was charged successfully and generated the estimated target field of 1.75 T at 5 K with the proposed PCS operation. During initial persistent-mode, the field was slightly decayed due to the index dissipation of the joint; thereafter it sustained the persistent field of 1.7 T for 35 h. The test results validated the joint resistance of < 1.2 × 10-11 as well as the proposed approach involving the PCS coil circuit model.

Assembly and Test of a 3-Nested-Coil 800-MHz REBCO Insert (H800) for the MIT 1.3 GHz LTS/HTS NMR Magnet

We present assembly and test results of a 3-nested-coil 800-MHz (18.8 T) REBCO insert (H800) for the MIT 1.3 GHz LTS/HTS NMR magnet currently under completion. Each of the three H800 coils is a stack of no-insulation (NI) REBCO double-pancake coils (DPs). The innermost 8.7-T Coil 1 (26 DPs) was completed by mid-2016; the middle 5.6-T Coil 2 (32 DPs) was complet-ed in mid-2017; while the outermost 4.5-T Coil 3 (38 DPs) was completed in early 2018. Coils 1, 2 & 3 were assembled together in early 2018 as a 3-nested-coil, the H800, and tested, first in liquid nitrogen to a power supply current of 20 A, followed by testing in liquid helium to a power supply current of 251.3 A, the H800's design operating current. After roughly five minutes settling time at 251.3 A, the H800 quenched. In this paper we examine probable sources of quench initiation and simulate ensuing quench behavior. Remedial efforts to minimize the tendency towards quenching in the H800 are presented and discussed.

Quench Analyses of the MIT 1.3-GHz LTS/HTS NMR Magnet

The MIT 1.3-GHz LTS/HTS NMR magnet is currently under development. The unique features of this magnet include a 3-nested formation for an 800-MHz REBCO insert (H800) and the no-insulation (NI) winding technique for H800 coils. Because when it is driven to the normal state, an NI REBCO magnet will respond electromagnetically, thermally, and mechanically that may result in permanent magnet damage, analysis of a quenching magnet is a key aspect of HTS magnet protection. We have developed a partial element equivalent circuit method coupled to a thermal and stress finite element method to analyze electromagnetic and mechanical responses of a nested-coil REBCO magnet each a stack of NI pancake coils. Using this method, quench simulations of the MIT 1.3-GHz LTS (L500)/HTS (H800) NMR magnet (1.3G), we have evaluated currents, strains, and torques of H800 Coil 1 to Coil 3 and L500, and center fields of 1.3G, L500, and H800. Our analyses show H800 is vulnerable to mechanical damage.

A novel Waikavirus (the family Secoviridae) genome sequence identified in rapeseed (Brassica napus)

The genome sequence of a novel species of the genus Waikavirus (the family Secoviridae), which we named Brassica napus RNA virus 1 (BnRV1), was identified in a rapeseed (Brassica napus) transcriptome dataset. The BnRV1 genome was 12,293 nucleotides long followed by a poly(A) tail. Two open reading frames (ORFs), called ORF1 and ORFX, were predicted. The larger ORF, ORF1, encodes a polyprotein of 3,471 amino acids and the smaller ORF, ORFX, overlaps ORF1 and encodes an 87 aa long protein of unknown function. The BnRV1 ORF1 polyprotein was predicted to undergo proteolytic processing to yield seven mature proteins, including an RNA-dependent RNA polymerase and three distinct coat proteins. The ORF1 and ORFX proteins share sequence similarities with the respective proteins of viruses in the genus Waikavirus, including the bellflower vein chlorosis virus, rice tungro spherical virus, and maize chlorotic dwarf virus. A phylogenetic tree inferred from a conserved segment of the polyproteins of several Secoviridae viruses confirmed that BnRV1 is a novel species of the genus Waikavirus. The BnRV1 genome sequence identified in this study may be useful for the study of waikavirus biology and waikavirus-derived diseases. Keywords: Brassica napus RNA virus 1; Waikavirus; Secoviridae; rapeseed.

Design of a Tabletop Liquid-Helium-Free 23.5-T Magnet Prototype towards 1-GHz Microcoil NMR

We present a design study of a liquid-helium (LHe)-free 23.5-T, ϕ25-mm RT-bore REBCO magnet for high-resolution 1-GHz microcoil nuclear magnetic resonance (NMR) spectroscopy. A microcoil NMR magnet is compact and thus its cost will be less by nearly an order of magnitude than that of the standard NMR magnet, and placeable on a bench, thereby resulting in a large saving in space. In addition, LHe-free operation enables the user to be independent from a cooling source in short supply. This paper includes: 1) magnet design and conductor requirement specification; 2) conceptual design of a full-scale tabletop LHe-free 1-GHz NMR magnet; and 3) design of a 10-K operating REBCO 23.5-T magnet prototype with a ϕ20-mm cold-bore. This small-size magnet prototype will be built and tested by 2020 for validation of performance and manufacturing challenges such as splices between coils. The paper concludes with discussion of stray-field shielding methods and a screening-current-inducing field (SCF) effect.

Blastacervulus metrosideri sp. nov. leaf spot on Metrosideros excelsa in New Zealand

A leaf-spotting fungal pathogen common on Metrosideros excelsa in New Zealand is described here as Blastacervulus metrosideri sp. nov. It has previously been identified in the New Zealand literature as Leptomelanconium sp. and as Staninwardia breviuscula. The choice of genus for this new species is supported by a phylogeny based on ITS and LSU sequences. It is phylogenetically close to several morphologically similar Eucalyptus leaf spotting pathogens.

Abstract P2-09-07: Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC)

Background: Radiation therapy (RT) induces immune-mediated cell death and could generate a rich supply of tumor antigens if administered in the pre-operative, curative-intent setting. The addition of PD-1 mediated checkpoint blockade to pre-operative RT could thus, generate robust anti-tumor immune responses, induce long-term tumor-specific memory, and ultimately, improve cure rates. This study aims to establish the safety of pre-operative pembrolizumab (pembro)-mediated immune modulation with a RT “boost” equivalent in patients with operable triple negative breast cancer (TNBC) for whom lumpectomy and adjuvant RT are planned (NCT03366844). Serial research biopsies permit interrogation of conventional biomarkers including tumor infiltrating lymphocytes (TILs) and novel immune correlates as potential predictors of response to pembro alone versus pembro with RT.

Methods: Ten women with operable, primary TNBC &gt;2cm for whom breast-conserving therapy is planned are being enrolled in this single-institution pilot study. Study treatment consists of 1 cycle of pre-operative pembro (200 mg IV) alone, followed 3 weeks later by a RT boost (24 Gy/3 fractions) to the primary breast tumor concurrently with pembro (+/- 5 days). Curative-intent, standard-of-care, neoadjuvant chemotherapy (NAC) or breast-conserving surgery is then undertaken within 8 weeks of study enrollment (i.e. within 5 weeks of pembro #2). Adjuvant RT is administered per standard-of-care after surgery, but without a boost dose. Research blood and fresh tumor biopsies are obtained at baseline and after cycles 1 and 2 of pembro. Co-primary endpoints are: 1) safety/tolerability, as defined by the number of patients who do not necessitate a delay in standard-of-care chemotherapy or surgery and 2) change in TIL score. Secondary endpoints include safety/toxicity up to 19 weeks after study enrollment, pCR rates and disease-free survival. Correlative analysis will include single-cell RNA sequencing of the tumor immune infiltrate and multispectral immunohistochemistry

Results: Seven patients enrolled between 12/19/17 and 7/1/18. As of 7/1/18, 5 patients have completed the experimental pembro/RT phase of the trial and are currently completing standard-of-care NAC; 1 patient is currently being treated in the experimental pembro/RT phase; and 1 patient with a cT2N0 tumor at baseline achieved a pathologic complete response (pCR, ypT0/Tis ypN0) after completing the experimental pembro/RT phase followed by anthracycline- and taxane-based NAC. No grade 3 or 4 toxicities have been observed during pembro/RT in the 6 patients completing the experimental phase to date. Three additional patients will be enrolled

Conclusions: This is the first trial of curative-intent, pre-operative checkpoint blockade with RT in breast cancer and the strategy appears to be well tolerated to date. At the time of presentation, safety, change in TIL score, and pCR rates for all patients completing the experimental and NAC phases of the study will be reported.

Citation Format: McArthur HL, Basho R, Shiao SL, Park D, Mita M, Chung A, Arnold B, Martin C, Dang C, Karlan S, Knott S, Giuliano A, Ho A. Preoperative pembrolizumab (Pembro) with radiation therapy (RT) in patients with operable triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-09-07.

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus

Amalgaviridae is a family of double-stranded, monosegmented RNA viruses that are associated with plants, fungi, microsporidians, and animals. A sequence contig derived from the transcriptome of a eudicot, Cistus incanus (the family Cistaceae; commonly known as hoary rockrose), was identified as the genome sequence of a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1). Sequence comparison and phylogenetic analysis indicated that CiRV1 is a novel species of the genus Amalgavirus in the family Amalgaviridae. The CiRV1 genome contig has two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. An ORF1+2 fusion protein, which functions in viral RNA replication, is produced by a +1 programmed ribosomal frameshifting (PRF) mechanism. A +1 PRF motif UUU_CGU, which matches the conserved amalgavirus +1 PRF consensus sequence UUU_CGN, was found at the boundary of CiRV1 ORF1 and ORF2. Comparison of 25 amalgavirus ORF1+2 fusion proteins revealed that only three different positions within a 13-amino acid segment were recurrently used at the boundary, possibly being selected so as not to interfere with correct folding and function of the fusion protein. CiRV1 is the first virus found to be associated with the Cistus species and may be useful for studying amalgaviruses.

Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum)

Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.