The photonics and optics workforce: unleashing the potential for greater industry growth-introduction to the feature issue.

This feature issue highlights specific photonics and optics workforce challenges, opportunities for industry support, and state-of-the-art-training methods.

DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors.

Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.

Adaptable middle-skilled labor: a neglected roadblock to photonics industry growth.

A roadblock to long-term growth of the photonics industry is the availability of well-trained, adaptable middle-skilled workers. This research characterizes the middle-skilled workforce gap, including the quantity required and skills needed. We estimate that 42,000 new technical middle-skilled workers are needed by 2030, requiring another 100 technician programs nationwide. Training skills along the supply chain are critical; programs must emphasize testing, troubleshooting, and process design. Middle-skilled workers trained in critical thinking will enable an adaptable workforce capable of handling technology evolution. Finally, recommendations for the academia, industry, and middle-skilled training ecosystem are included to ensure that the latter evolves with technology development.

Clearance of plasma PCSK9 via the asialoglycoprotein receptor mediated by heterobifunctional ligands.

Proprotein convertase subtilisin/kexin type 9 (PCSK9) regulates plasma low-density lipoprotein cholesterol (LDL-C) levels by promoting the degradation of hepatic LDL receptors (LDLRs). Current therapeutic approaches use antibodies that disrupt PCSK9 binding to LDLR to reduce circulating LDL-C concentrations or siRNA that reduces PCSK9 synthesis and thereby levels in circulation. Recent reports describe small molecules that, like therapeutic antibodies, interfere with PCSK9 binding to LDLR. We report an alternative approach to decrease circulating PCSK9 levels by accelerating PCSK9 clearance and degradation using heterobifunctional molecules that simultaneously bind to PCSK9 and the asialoglycoprotein receptor (ASGPR). Various formats, including bispecific antibodies, antibody-small molecule conjugates, and heterobifunctional small molecules, demonstrate binding in vitro and accelerated PCSK9 clearance in vivo. These molecules showcase a new approach to PCSK9 inhibition, targeted plasma protein degradation (TPPD), and demonstrate the feasibility of heterobifunctional small molecule ligands to accelerate the clearance and degradation of pathogenic proteins in circulation.

Development of a Standardized Assessment of Simulation-based Extracorporeal Membrane Oxygenation Educational Courses.

Background: In 2020, the Extracorporeal Life Support Organization education task force identified seven extracorporeal membrane oxygenation (ECMO) educational domains that would benefit from international collaborative efforts. These included research efforts to delineate the impact and outcomes of ECMO courses. Objective: Development of a standardized online assessment tool to evaluate the effectiveness of didactic and simulation-based ECMO courses on participants' confidence, knowledge, and simulation-based skills; participant satisfaction; and course educational benefits. Methods: We performed a prospective multicenter observational study of five different U.S. academic institution-based adult ECMO courses that met Extracorporeal Life Support Organization endorsement requirements for course structure, educational content, and objectives. Standardized online forms were developed and administered before and after courses, assessing demographics, self-assessment regarding ECMO management, and knowledge examination (15 simple-recall multiple-choice questions). Psychomotor skill assessment was performed during the course (time to complete prespecified critical actions during simulation scenarios). Self-assessment evaluated cognitive, behavioral, and technical aspects of ECMO; course satisfaction; and educational benefits. Results: Out of 211 participants, 107 completed both pre- and postcourse self-assessment forms (97 completed both pre- and postcourse knowledge forms). Fifty-three percent of respondents were physician intensivists, with most (51%) practicing at academic hospitals and with less than 1 year of ECMO experience (50%). After the course, participants reported significant increases in confidence across all domains (cognitive, technical, and behavioral, P < 0.0001, 95% confidence interval [CI], 1.2-1.5; P < 0.0001, 95% CI, 2.2-2.6; and P = 0.002, 95% CI, 1.7-2.1, respectively) with an increase in knowledge scores (P < 0.001; 95% CI, 1.4-2.5). These findings were most significant in participants with less ECMO experience. There were also significant reductions in times to critical actions in three of the four scored simulation scenarios. The results demonstrated participants' satisfaction with most course aspects, with more than 95% expressing that courses met their educational goals. Conclusion: We developed and tested a structured ECMO course assessment tool, demonstrating participants' self-reported benefit as well as improvement in psychomotor skill acquisition, course satisfaction, and educational benefits. Course evaluation is feasible and potentially provides important information to improve ECMO courses. Future steps could include national implementation, addition of questions targeting clinical decision making to further assess knowledge gain, and multilanguage translation for implementation in international courses.

Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels.

Amino acid substitutions in the exonuclease domain of DNA polymerase ϵ (Polϵ) cause ultramutated tumors. Studies in model organisms suggested pathogenic mechanisms distinct from a simple loss of exonuclease. These mechanisms remain unclear for most recurrent Polϵ mutations. Particularly, the highly prevalent V411L variant remained a long-standing puzzle with no detectable mutator effect in yeast despite the unequivocal association with ultramutation in cancers. Using purified four-subunit yeast Polϵ, we assessed the consequences of substitutions mimicking human V411L, S459F, F367S, L424V and D275V. While the effects on exonuclease activity vary widely, all common cancer-associated variants have increased DNA polymerase activity. Notably, the analog of Polϵ-V411L is among the strongest polymerases, and structural analysis suggests defective polymerase-to-exonuclease site switching. We further show that the V411L analog produces a robust mutator phenotype in strains that lack mismatch repair, indicating a high rate of replication errors. Lastly, unlike wild-type and exonuclease-dead Polϵ, hyperactive variants efficiently synthesize DNA at low dNTP concentrations. We propose that this characteristic could promote cancer cell survival and preferential participation of mutator polymerases in replication during metabolic stress. Our results support the notion that polymerase fitness, rather than low fidelity alone, is an important determinant of variant pathogenicity.

Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-l-glutamic Acid-coated Layer-by-Layer Nanoparticles.

The oncogenic transcription factor STAT3 is aberrantly activated in 70% of breast cancers, including nearly all triple-negative breast cancers (TNBCs). Because STAT3 is difficult to target directly, we considered whether metabolic changes driven by activated STAT3 could provide a therapeutic opportunity. We found that STAT3 prominently modulated several lipid classes, with most profound effects on N-acyl taurine and arachidonic acid, both of which are involved in plasma membrane remodeling. To exploit these metabolic changes therapeutically, we screened a library of layer-by-layer (LbL) nanoparticles (NPs) differing in the surface layer that modulates interactivity with the cell membrane. We found that poly-l-glutamic acid (PLE)-coated NPs bind to STAT3-transformed breast cancer cells with 50% greater efficiency than to nontransformed cells, and the heightened PLE-NP binding to TNBC cells was attenuated by STAT3 inhibition. This effect was also observed in densely packed three-dimensional breast cancer organoids. As STAT3-transformed cells show greater resistance to cytotoxic agents, we evaluated whether enhanced targeted delivery via PLE-NPs would provide a therapeutic advantage. We found that cisplatin-loaded PLE-NPs induced apoptosis of STAT3-driven cells at lower doses compared with both unencapsulated cisplatin and cisplatin-loaded nontargeted NPs. In addition, because radiation is commonly used in breast cancer treatment, and may alter cellular lipid distribution, we analyzed its effect on PLE-NP-cell binding. Irradiation of cells enhanced the STAT3-targeting properties of PLE-NPs in a dose-dependent manner, suggesting potential synergies between these therapeutic modalities. These findings suggest that cellular lipid changes driven by activated STAT3 may be exploited therapeutically using unique LbL NPs.

A Virtual Multidisciplinary Care Program for Management of Advanced Chronic Kidney Disease: Matched Cohort Study.

BACKGROUND: It is not well established whether a virtual multidisciplinary care program for persons with advanced chronic kidney disease (CKD) can improve their knowledge about their disease, increase their interest in home dialysis therapies, and result in more planned outpatient (versus inpatient) dialysis starts. OBJECTIVE: We aimed to evaluate the feasibility and preliminary associations of program participation with disease knowledge, home dialysis modality preference, and outpatient dialysis initiation among persons with advanced CKD in a community-based nephrology practice. METHODS: In a matched prospective cohort, we enrolled adults aged 18 to 85 years with at least two estimated glomerular filtration rates (eGFRs) of less than 30 mL/min/1.73 m2 into the Cricket Health program and compared them with controls receiving care at the same clinic, matched on age, gender, eGFR, and presence of heart failure and diabetes. The intervention included online education materials, a virtual multidisciplinary team (nurse, pharmacist, social worker, dietician), and patient mentors. Prespecified follow-up time was nine months with extended follow-up to allow adequate time to determine the dialysis start setting. CKD knowledge and dialysis modality choice were evaluated in a pre-post survey among intervention participants. RESULTS: Thirty-seven participants were matched to 61 controls by age (mean 67.2, SD 10.4 versus mean 68.8, SD 9.5), prevalence of diabetes (54%, 20/37 versus 57%, 35/61), congestive heart failure (22%, 8/37 versus 25%, 15/61), and baseline eGFR (mean 19, SD 6 versus mean 21, SD 5 mL/min/1.73 m2), respectively. At nine-month follow-up, five patients in each group started dialysis (P=.62). Among program participants, 80% (4/5) started dialysis as an outpatient compared with 20% (1/5) of controls (OR 6.28, 95% CI 0.69-57.22). In extended follow-up (median 15.7, range 11.7 to 18.1 months), 19 of 98 patients started dialysis; 80% (8/10) of the intervention group patients started dialysis in the outpatient setting versus 22% (2/9) of control patients (hazard ratio 6.89, 95% CI 1.46-32.66). Compared to before participation, patients who completed the program had higher disease knowledge levels (mean 52%, SD 29% versus mean 94%, SD 14% of questions correct on knowledge-based survey, P<.001) and were more likely to choose a home modality as their first dialysis choice (36%, 7/22 versus 68%, 15/22, P=.047) after program completion. CONCLUSIONS: The Cricket Health program can improve patient knowledge about CKD and increase interest in home dialysis modalities, and may increase the proportion of dialysis starts in the outpatient setting.

Comment on "A commensal strain of Staphylococcus epidermidis protects against skin neoplasia" by Nakatsuji et al.

A recent article in Science Advances described the striking discovery that the commensal Staphylococcus epidermidis strain MO34 displays antimicrobial and antitumor activities by producing a small molecule, identified as the nucleobase analog 6-N-hydroxylaminopurine (6-HAP). However, in contradiction to the literature, the authors claimed that 6-HAP is nonmutagenic and proposed that the toxic effect of 6-HAP results from its ability to inhibit, in its base form, DNA synthesis. To resolve the discrepancy, we proved by genetic experiments with bacteria and yeast that extracts of MO34 do contain a mutagenic compound whose effects are identical to chemically synthesized 6-HAP. The MO34 extract induced the same mutation spectrum as authentic 6-HAP. Notably, the toxic and mutagenic effects of both synthetic and MO34-derived 6-HAP depended on conversion to the corresponding nucleotide. The nucleobase 6-HAP does not inhibit DNA synthesis in vitro, and we conclude that 6-HAP exerts its biological activity when incorporated into DNA.

Fullerene toxicity in the benthos with implications for freshwater ecosystem services.

Production of engineered carbon-based nanomaterials (CNMs) is rising, with increased risk of release to the environment during production, use, and disposal. This trend highlights a need to understand potential impacts of CNMs on the natural environment. Fullerenes are an emerging class of CNMs that are insoluble in water, and form aggregates that settle quickly, suggesting higher relative vulnerability of aquatic benthic ecosystems. This study assessed eco-toxicity of fullerenes (C60, C70) and the functionalized derivative, phenyl-C61-butyric acid methyl ester (PCBM), on functionally representative benthic organisms in traditional laboratory assays, and evaluated how the potential lethal and sub-lethal effects of fullerenes may indirectly impact benthic ecosystem function, including decomposition, primary productivity and nutrient cycling in lake microcosms with natural sediments. Standard toxicity tests indicated that population growth of Lumbriculus variegatus was reduced at 25 to 150 mg C60 kg-1, but C70 and PCBM did not affect growth or weight of organisms in artificial sediments at 25 mg kg-1. Survivorship and growth were lower in natural sediments with historic contamination, but C60 did not exacerbate this effect. C60 inhibited photosynthesis by the benthic diatom Nitzschia palea, and at high exposure chlorophyll a increased, suggesting a shading response. L. variegatus had strong effects on benthic ecosystem function, especially metabolism and nitrogen cycling, but C60 ≤ 30 mg kg-1 sediment did not influence the role of L. variegatus in driving benthic processes. These observations suggest that at moderate to high concentrations, C60 may directly impact benthic organisms. However, under natural conditions with low to moderate concentrations, C60 has little effect and does not indirectly impact the ecosystem processes maintained by such organisms. These results are a step further towards a better understanding of potential impacts of fullerenes on aquatic ecosystems, and can aid in the development of regulatory policies.

Cascading Ecological Impacts of Fullerenes in Freshwater Ecosystems.

Carbonaceous nanomaterials, such as fullerenes (C60, C70) and the derivative phenyl-C61-butyric acid methyl ester (PCBM), have promising application in solar energy technologies. Although the acute ecotoxicity of C60 has been reported widely in the literature, ecotoxicity assays for different fullerene forms and broader ecosystem impact studies remain scarce. To address these knowledge gaps, acute, chronic, and life stage exposure studies with freshwater zooplankton, Daphnia magna and Daphnia pulex, were performed for each material. Experimental results indicated that C60 and PCBM are not acutely toxic at estimated environmentally relevant concentrations; however, C70 had significant acute effects. All forms of fullerene caused a gradual elevation in heart rate over time and visual darkening of the Daphnia spp. carapace. The impact of fullerenes on susceptibility to predation was then assessed experimentally by presenting D. pulex to the visual predator Lepomis macrochirus (bluegill). Predation risk was significantly increased in fullerene-exposed D. pulex. The present study underscores the need to broaden the scope of traditional ecotoxicity for emerging materials: studies are required that evaluate portfolios of related nanomaterials and that capture chronic and cascading ecosystem-level effects. Environ Toxicol Chem 2019;38:1714-1723. © 2019 SETAC.

A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme.

Alterations in the exonuclease domain of DNA polymerase ε (Polε) cause ultramutated tumors. Severe mutator effects of the most common variant, Polε-P286R, modeled in yeast suggested that its pathogenicity involves yet unknown mechanisms beyond simple proofreading deficiency. We show that, despite producing a catastrophic amount of replication errors in vivo, the yeast Polε-P286R analog retains partial exonuclease activity and is more accurate than exonuclease-dead Polε. The major consequence of the arginine substitution is a dramatically increased DNA polymerase activity. This is manifested as a superior ability to copy synthetic and natural templates, extend mismatched primer termini, and bypass secondary DNA structures. We discuss a model wherein the cancer-associated substitution limits access of the 3'-terminus to the exonuclease site and promotes binding at the polymerase site, thus stimulating polymerization. We propose that the ultramutator effect results from increased polymerase activity amplifying the contribution of Polε errors to the genomic mutation rate.

Portfolio Optimization of Nanomaterial Use in Clean Energy Technologies.

While engineered nanomaterials (ENMs) are increasingly incorporated in diverse applications, risks of ENM adoption remain difficult to predict and mitigate proactively. Current decision-making tools do not adequately account for ENM uncertainties including varying functional forms, unique environmental behavior, economic costs, unknown supply and demand, and upstream emissions. The complexity of the ENM system necessitates a novel approach: in this study, the adaptation of an investment portfolio optimization model is demonstrated for optimization of ENM use in renewable energy technologies. Where a traditional investment portfolio optimization model maximizes return on investment through optimal selection of stock, ENM portfolio optimization maximizes the performance of energy technology systems by optimizing selective use of ENMs. Cumulative impacts of multiple ENM material portfolios are evaluated in two case studies: organic photovoltaic cells (OPVs) for renewable energy and lithium-ion batteries (LIBs) for electric vehicles. Results indicate ENM adoption is dependent on overall performance and variance of the material, resource use, environmental impact, and economic trade-offs. From a sustainability perspective, improved clean energy applications can help extend product lifespans, reduce fossil energy consumption, and substitute ENMs for scarce incumbent materials.

Functional Analysis of Cancer-Associated DNA Polymerase ε Variants in Saccharomyces cerevisiae.

DNA replication fidelity relies on base selectivity of the replicative DNA polymerases, exonucleolytic proofreading, and postreplicative DNA mismatch repair (MMR). Ultramutated human cancers without MMR defects carry alterations in the exonuclease domain of DNA polymerase ε (Polε). They have been hypothesized to result from defective proofreading. However, modeling of the most common variant, Polε-P286R, in yeast produced an unexpectedly strong mutator effect that exceeded the effect of proofreading deficiency by two orders of magnitude and indicated the involvement of other infidelity factors. The in vivo consequences of many additional Polε mutations reported in cancers remain poorly understood. Here, we genetically characterized 13 cancer-associated Polε variants in the yeast system. Only variants directly altering the DNA binding cleft in the exonuclease domain elevated the mutation rate. Among these, frequently recurring variants were stronger mutators than rare variants, in agreement with the idea that mutator phenotype has a causative role in tumorigenesis. In nearly all cases, the mutator effects exceeded those of an exonuclease-null allele, suggesting that mechanisms distinct from loss of proofreading may drive the genome instability in most ultramutated tumors. All mutator alleles were semidominant, supporting the view that heterozygosity for the polymerase mutations is sufficient for tumor development. In contrast to the DNA binding cleft alterations, peripherally located variants, including a highly recurrent V411L, did not significantly elevate mutagenesis. Finally, the analysis of Polε variants found in MMR-deficient tumors suggested that the majority cause no mutator phenotype alone but some can synergize with MMR deficiency to increase the mutation rate.

Simultaneous measurement of temperature, stress, and electric field in GaN HEMTs with micro-Raman spectroscopy.

As semiconductor devices based on silicon reach their intrinsic material limits, compound semiconductors, such as gallium nitride (GaN), are gaining increasing interest for high performance, solid-state transistor applications. Unfortunately, higher voltage, current, and/or power levels in GaN high electron mobility transistors (HEMTs) often result in elevated device temperatures, degraded performance, and shorter lifetimes. Although micro-Raman spectroscopy has become one of the most popular techniques for measuring localized temperature rise in GaN HEMTs for reliability assessment, decoupling the effects of temperature, mechanical stress, and electric field on the optical phonon frequencies measured by micro-Raman spectroscopy is challenging. In this work, we demonstrate the simultaneous measurement of temperature rise, inverse piezoelectric stress, thermoelastic stress, and vertical electric field via micro-Raman spectroscopy from the shifts of the E2 (high), A1 longitudinal optical (LO), and E2 (low) optical phonon frequencies in wurtzite GaN. We also validate experimentally that the pinched OFF state as the unpowered reference accurately measures the temperature rise by removing the effect of the vertical electric field on the Raman spectrum and that the vertical electric field is approximately the same whether the channel is open or closed. Our experimental results are in good quantitative agreement with a 3D electro-thermo-mechanical model of the HEMT we tested and indicate that the GaN buffer acts as a semi-insulating, p-type material due to the presence of deep acceptors in the lower half of the bandgap. This implementation of micro-Raman spectroscopy offers an exciting opportunity to simultaneously probe thermal, mechanical, and electrical phenomena in semiconductor devices under bias, providing unique insight into the complex physics that describes device behavior and reliability. Although GaN HEMTs have been specifically used in this study to demonstrate its viability, this technique is applicable to any solid-state material with a suitable Raman response and will likely enable new measurement capabilities in a wide variety of scientific and engineering applications.

Flexible Gallium Nitride for High-Performance, Strainable Radio-Frequency Devices.

Flexible gallium nitride (GaN) thin films can enable future strainable and conformal devices for transmission of radio-frequency (RF) signals over large distances for more efficient wireless communication. For the first time, strainable high-frequency RF GaN devices are demonstrated, whose exceptional performance is enabled by epitaxial growth on 2D boron nitride for chemical-free transfer to a soft, flexible substrate. The AlGaN/GaN heterostructures transferred to flexible substrates are uniaxially strained up to 0.85% and reveal near state-of-the-art values for electrical performance, with electron mobility exceeding 2000 cm2 V-1 s-1 and sheet carrier density above 1.07 × 1013 cm-2 . The influence of strain on the RF performance of flexible GaN high-electron-mobility transistor (HEMT) devices is evaluated, demonstrating cutoff frequencies and maximum oscillation frequencies greater than 42 and 74 GHz, respectively, at up to 0.43% strain, representing a significant advancement toward conformal, highly integrated electronic materials for RF applications.

Novel Utilization of the Bridge During Weaning Off Venoarterial ECMO: The Hoffman Clamp Method.

Standard practice for weaning patients off venoarterial extracorporeal membrane oxygenation (ECMO) occurs by decreasing pump flows until idle flow is achieved. This method is limited in its use because it is difficult to assess a patient's true potential to successfully come off ECMO when supported by idle flow. We have developed a weaning technique that uses a Hoffman clamp on the bridge to decrease blood flow to the patient beyond idle flow. This method was used to wean eight patients from venoarterial ECMO. No patients weaned with this technique required emergent reinstitution of ECMO. The Hoffman clamp technique has allowed us to safely wean patients off ECMO support while maintaining integrity of the circuit.