Recent advances in the SISSO method and their implementation in the SISSO++ code.

Accurate and explainable artificial-intelligence (AI) models are promising tools for accelerating the discovery of new materials. Recently, symbolic regression has become an increasingly popular tool for explainable AI because it yields models that are relatively simple analytical descriptions of target properties. Due to its deterministic nature, the sure-independence screening and sparsifying operator (SISSO) method is a particularly promising approach for this application. Here, we describe the new advancements of the SISSO algorithm, as implemented into SISSO++, a C++ code with Python bindings. We introduce a new representation of the mathematical expressions found by SISSO. This is a first step toward introducing "grammar" rules into the feature creation step. Importantly, by introducing a controlled nonlinear optimization to the feature creation step, we expand the range of possible descriptors found by the methodology. Finally, we introduce refinements to the solver algorithms for both regression and classification, which drastically increase the reliability and efficiency of SISSO. For all these improvements to the basic SISSO algorithm, we not only illustrate their potential impact but also fully detail how they operate both mathematically and computationally.

Anharmonicity in Thermal Insulators: An Analysis from First Principles.

The anharmonicity of atomic motion limits the thermal conductivity in crystalline solids. However, a microscopic understanding of the mechanisms active in strong thermal insulators is lacking. In this Letter, we classify 465 experimentally known materials with respect to their anharmonicity and perform fully anharmonic ab initio Green-Kubo calculations for 58 of them, finding 28 thermal insulators with κ<10 W/mK including 6 with ultralow κ≲1 W/mK. Our analysis reveals that the underlying strong anharmonic dynamics is driven by the exploration of metastable intrinsic defect geometries. This is at variance with the frequently applied perturbative approach, in which the dynamics is assumed to evolve around a single stable geometry.

Hierarchical Symbolic Regression for Identifying Key Physical Parameters Correlated with Bulk Properties of Perovskites.

Symbolic regression identifies nonlinear, analytical expressions relating materials properties and key physical parameters. However, the pool of expressions grows rapidly with complexity, compromising its efficiency. We tackle this challenge hierarchically: identified expressions are used as inputs for further obtaining more complex expressions. Crucially, this framework can transfer knowledge among properties, as demonstrated using the sure-independence-screening-and-sparsifying-operator approach to identify expressions for lattice constant and cohesive energy, which are then used to model the bulk modulus of ABO_{3} perovskites.

Durvalumab with platinum-pemetrexed for unresectable pleural mesothelioma: survival, genomic and immunologic analyses from the phase 2 PrE0505 trial.

Mesothelioma is a rare and fatal cancer with limited therapeutic options until the recent approval of combination immune checkpoint blockade. Here we report the results of the phase 2 PrE0505 trial ( NCT02899195 ) of the anti-PD-L1 antibody durvalumab plus platinum-pemetrexed chemotherapy for 55 patients with previously untreated, unresectable pleural mesothelioma. The primary endpoint was overall survival compared to historical control with cisplatin and pemetrexed chemotherapy; secondary and exploratory endpoints included safety, progression-free survival and biomarkers of response. The combination of durvalumab with chemotherapy met the pre-specified primary endpoint, reaching a median survival of 20.4 months versus 12.1 months with historical control. Treatment-emergent adverse events were consistent with known side effects of chemotherapy, and all adverse events due to immunotherapy were grade 2 or lower. Integrated genomic and immune cell repertoire analyses revealed that a higher immunogenic mutation burden coupled with a more diverse T cell repertoire was linked to favorable clinical outcome. Structural genome-wide analyses showed a higher degree of genomic instability in responding tumors of epithelioid histology. Patients with germline alterations in cancer predisposing genes, especially those involved in DNA repair, were more likely to achieve long-term survival. Our findings indicate that concurrent durvalumab with platinum-based chemotherapy has promising clinical activity and that responses are driven by the complex genomic background of malignant pleural mesothelioma.

OPTIMADE, an API for exchanging materials data.

The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.

Modeling optical coupling of plasmons and inhomogeneously broadened emitters.

Optically coupling quantum emitters to nanoparticles provides the foundation for many plasmonic applications. Including quantum mechanical effects within the calculations can be crucial for designing new devices, but classical approximations are sometimes sufficient. Comprehending how the classical and quantum mechanical descriptions of quantum emitters alter their calculated optical response will lead to a better understanding of how to design devices. Here, we describe how the semiclassical Maxwell-Liouville method can be used to calculate the optical response from inhomogeneously broadened states. After describing the Maxwell-Liouville algorithm, we use the method to study the photon echoes from quantum dots and compare the results against analytical models. We then modify the quantum dot's state distribution to match a PbS 850 nm quantum dot's absorption spectra to see how the complete quasi-band structure affects their coupling to gold nanoislands. Finally, we compare the results with previously published work to demonstrate where the complete quantum dot description is necessary.

Natural History and Factors Associated with Overall Survival in Stage IV ALK-Rearranged Non-Small Cell Lung Cancer.

INTRODUCTION: Clinical variables describing the natural history and longitudinal therapy outcomes of stage IV anaplastic lymphoma kinase gene rearrangement positive (ALK-positive) NSCLC and their relationship with long-term overall survival (OS) have not previously been described in detail. METHODS: Patients with stage IV NSCLC treated with an ALK inhibitor at the University of Colorado Cancer Center from 2009 through November 2017 were identified retrospectively. OS curves were constructed by using Kaplan-Meier methods. Multivariate Cox proportional hazard analysis was used to determine the relationship of variables with OS. RESULTS: Of the 110 patients with ALK-positive NSCLC who were identified, 105 received crizotinib as their initial ALK inhibitor. With a median follow-up time of 47 months, the median OS time from diagnosis of stage IV disease was 81 months (6.8 years). Brain metastases at diagnosis of stage IV disease (hazard ratio = 1.01, p = 0.971) and year of stage IV presentation (p = 0.887) did not influence OS. More organs with tumor at diagnosis of stage IV disease was associated with worse OS (HR = 1.49 for each additional organ with disease, including the CNS [p = 0.002]). Each additional month of pemetrexed-based therapy was associated with a 7% relative decrease in risk of death. CONCLUSION: Patients with stage IV ALK-positive NSCLC can have prolonged OS. Brain metastases at diagnosis of stage IV disease does not influence OS. Having more organs involved with tumor at stage IV presentation is associated with worse outcomes. Prolonged benefit from pemetrexed is associated with better outcomes.

Mapping of amino acid substitutions conferring herbicide resistance in wheat glutathione transferase.

We have used design of experiments (DOE) and systematic variance to efficiently explore glutathione transferase substrate specificities caused by amino acid substitutions. Amino acid substitutions selected using phylogenetic analysis were synthetically combined using a DOE design to create an information-rich set of gene variants, termed infologs. We used machine learning to identify and quantify protein sequence-function relationships against 14 different substrates. The resulting models were quantitative and predictive, serving as a guide for engineering of glutathione transferase activity toward a diverse set of herbicides. Predictive quantitative models like those presented here have broad applicability for bioengineering.

Easily reducible materials from the reactions of diselenopheno[3,2-b:2',3'-d]pyrrole and dithieno[3,2-b:2',3'-d]pyrrole with tetracyanoethylene.

A new core, 4H-diselenopheno[3,2-b:2',3'-d]pyrrole (DSP), was reacted with tetracyanoethylene, and three products, mono-tricyanovinyl, bis-tricyanovinyl, and quinoidal, were isolated and compared with the respective 4H-dithieno[3,2-b:2',3'-d]pyrrole (DTP) derivatives using cyclic voltammetry, UV-vis absorption, and differential scanning calorimetry analyses. Organic field-effect transistors were fabricated using solution-processed films, and only one derivative, bis-tricyanovinyl-DSP, exhibited transistor behavior with µ(e) reaching 8.7 × 10(-4) cm(2)/V·s. This enhancement of the electron-transporting properties in comparison with DTP derivative is attributed to stronger LUMO-LUMO interaction due to a larger size of selenium atom, which in the case of the bis-tricyanovinyl derivative, has wave function density on the chalcogen.

Optical traps to study properties of molecular motors.

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This article describes the use of optical traps to study processive and nonprocessive molecular motor proteins, focusing on the design of the instrument and the assays to characterize motility.

Attachment of anti-GFP antibodies to microspheres for optical trapping experiments.

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This protocol describes a method for attaching anti-GFP (green fluorescent protein) antibodies to microspheres. GFP-motor fusion proteins can then be adsorbed to the microspheres for use in single-molecule motility studies and optical trapping experiments.

The optical trapping dumbbell assay for nonprocessive motors or motors that turn around filaments.

In vitro motility assays enabled the analysis of coupling between ATP hydrolysis and movement of myosin along actin filaments or kinesin along microtubules. Single-molecule assays using laser trapping have been used to obtain more detailed information about kinesins, myosins, and processive DNA enzymes. The combination of in vitro motility assays with laser-trap measurements has revealed detailed dynamic structural changes associated with the ATPase cycle. This protocol describes the preparation of biotin-actin filaments and coverslips coated with polystyrene beads. These are then used in optical trapping dumbbell assays to study interactions between motors and filaments.

EPR spectra and molecular dynamics agree that the nucleotide pocket of myosin V is closed and that it opens on binding actin.

We have used EPR spectroscopy and computational modeling of nucleotide-analog spin probes to investigate conformational changes at the nucleotide site of myosin V. We find that, in the absence of actin, the mobility of a spin-labeled diphosphate analog [spin-labeled ADP (SLADP)] bound at the active site is strongly hindered, suggesting a closed nucleotide pocket. The mobility of the analog increases when the MV·SLADP complex (MV=myosin V) binds to actin, implying an opening of the active site in the A·MV·SLADP complex (A=actin). The probe mobilities are similar to those seen with myosin II, despite the fact that myosin V has dramatically altered kinetics. Molecular dynamics (MD) simulation was used to understand the EPR spectra in terms of the X-ray database. The X-ray structure of MV·ADP·BeFx shows a closed nucleotide site and has been proposed to be the detached state. The MV·ADP structure shows an open nucleotide site and has been proposed to be the A·MV·ADP state at the end of the working powerstroke. MD simulation of SLADP docked in the closed conformation gave a probe mobility comparable to that seen in the EPR spectrum of the MV·SLADP complex. The simulation of the open conformation gave a probe mobility that was 35-40° greater than that observed experimentally for the A·MV·SLADP state. Thus, EPR, X-ray diffraction, and computational analysis support the closed conformation as a myosin V state that is detached from actin. The MD results indicate that the MV·ADP crystal structure, which may correspond to the strained actin-bound post-powerstroke conformation resulting from head-head interaction in the dimeric processive motor, is superopened.

Nucleotide pocket thermodynamics measured by EPR reveal how energy partitioning relates myosin speed to efficiency.

We have used spin-labeled ADP to investigate the dynamics of the nucleotide-binding pocket in a series of myosins, which have a range of velocities. Electron paramagnetic resonance spectroscopy reveals that the pocket is in equilibrium between open and closed conformations. In the absence of actin, the closed conformation is favored. When myosin binds actin, the open conformation becomes more favored, facilitating nucleotide release. We found that faster myosins favor a more closed pocket in the actomyosin•ADP state, with smaller values of ΔH(0) and ΔS(0), even though these myosins release ADP at a faster rate. A model involving a partitioning of free energy between work-generating steps prior to rate-limiting ADP release explains both the unexpected correlation between velocity and opening of the pocket and the observation that fast myosins are less efficient than slow myosins.

Combining EPR with fluorescence spectroscopy to monitor conformational changes at the myosin nucleotide pocket.

We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectroscopy and tryptophan fluorescence have been used previously to investigate changes at the myosin nucleotide site. A limitation of fluorescence spectroscopy is that it must be done on mutated myosins containing only a single tryptophan. A limitation of EPR spectroscopy is that one infers protein conformational changes from alterations in the mobility of an attached probe. These limitations have led to controversies regarding conclusions reached by the two approaches. For the first time, the data presented here allow direct correlations to be made between the results from the two spectroscopic approaches on the same proteins and extend our previous EPR studies to a nonmuscle myosin. EPR probe mobility indicates that the conformation of the nucleotide pocket of the WTSLADP (spin-labeled ADP) complex is similar to that of skeletal myosin. The pocket is closed in the absence of actin for both diphosphate and triphosphate nucleotide states. In the actin myosin diphosphate state, the pocket is in equilibrium between closed and open conformations, with the open conformation slightly more favorable than that seen for fast skeletal actomyosin. The EPR spectra for the mutant show similar conformations to skeletal myosin, with one exception: in the absence of actin, the nucleotide pocket of the mutant displays an open component that was approximately 4-5 kJ/mol more favorable than in skeletal or WT myosin. These observations resolve the controversies between the two techniques. The data from both techniques confirm that binding of myosin to actin alters the conformation of the myosin nucleotide pocket with similar but not identical energetics in both muscle and nonmuscle myosins.

The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes.

Evenly spaced nucleosomes directly correlate with condensed chromatin and gene silencing. The ATP-dependent chromatin assembly factor (ACF) forms such structures in vitro and is required for silencing in vivo. ACF generates and maintains nucleosome spacing by constantly moving a nucleosome towards the longer flanking DNA faster than the shorter flanking DNA. How the enzyme rapidly moves back and forth between both sides of a nucleosome to accomplish bidirectional movement is unknown. Here we show that nucleosome movement depends cooperatively on two ACF molecules, indicating that ACF functions as a dimer of ATPases. Further, the nucleotide state determines whether the dimer closely engages one or both sides of the nucleosome. Three-dimensional reconstruction by single-particle electron microscopy of the ATPase-nucleosome complex in an activated ATP state reveals a dimer architecture in which the two ATPases face each other. Our results indicate a model in which the two ATPases work in a coordinated manner, taking turns to engage either side of a nucleosome, thereby allowing processive bidirectional movement. This novel dimeric motor mechanism differs from that of dimeric motors such as kinesin and dimeric helicases that processively translocate unidirectionally and reflects the unique challenges faced by motors that move nucleosomes.

Adaptation of Predictive Models to PDA Hand-Held Devices.

Prediction models using multiple logistic regression are appearing with increasing frequency in the medical literature. Problems associated with these models include the complexity of computations when applied in their pure form, and lack of availability at the bedside. Personal digital assistant (PDA) hand-held devices equipped with spreadsheet software offer the clinician a readily available and easily applied means of applying predictive models at the bedside. The purposes of this article are to briefly review regression as a means of creating predictive models and to describe a method of choosing and adapting logistic regression models to emergency department (ED) clinical practice.

Leukocytosis as a predictor of severe injury in blunt trauma.

OBJECTIVE: The objective of this study was to determine if the white blood cell count can predict severity of injury in blunt trauma victims. METHODS: This was a retrospective study comparing two groups of blunt trauma victims by severity of injury, one with significant injury and one without significant injury, and comparing their initial WBC in the emergency department (ED). We also examined if WBC correlates with degree of injury using Injury Severity Score (ISS) in both groups combined. Further, we examined the WBC as a predictor of serious injury. RESULTS: Our study showed a difference in mean WBC between the two groups that was statistically significant (p<0.001). A positive relationship between ISS and WBC was found, although the association was weak (correlation coefficient = 0.369). While the WBC had moderate discriminatory capability for serious injury, it could not, in isolation, reliably rule in or out serious injury. Nevertheless, this study supports using WBC on presentation to the ED as an adjunct for making disposition decisions. CONCLUSION: A significant elevation in WBC in a blunt trauma patient, even with minimal initial signs of severe injury, should heighten suspicion for occult injury.

Phase I and pharmacokinetic study of UCN-01 in combination with irinotecan in patients with solid tumors.

PURPOSE: 7-Hydroxystaurosporine (UCN-01) is a protein kinase inhibitor that inhibits several serine-threonine kinases including PKC and PDK1. Due to the preclinical synergistic effects seen with topoisomerase I inhibitors and non-overlapping toxicity, UCN-01 and irinotecan were combined in a dose-finding study designed to determine the maximum tolerated dose (MTD), toxicity profile, and pharmacokinetics (PK) of UCN-01 and irinotecan. METHODS: Patients with incurable solid malignancies received UCN-01 intravenously (IV) as a 3-h infusion on day 1 and irinotecan IV over 90 min on days 1 and 8 of a 21-day cycle. Doses of UCN-01 for subsequent cycles were half the starting dose. Dose level 1 (DL1) consisted of UCN-01 and irinotecan doses of 50 and 60 mg/m(2), respectively. Blood samples were collected in cycle 1 for UCN-01, irinotecan, and irinotecan metabolites. RESULTS: A total of 16 patients were enrolled on the trial at UCN-01/Irinotecan doses of 50/60 mg/m(2) (DL1; n = 1), 70/60 mg/m(2) (DL2; n = 6), 90/60 mg/m(2) (DL3; n = 4), and 70/90 mg/m(2) (DL4; n = 5). Two dose-limiting toxicities were observed each in DL3 and DL4 (2 grade 3 hypophosphatemia, 1 grade 4 hyperglycemia and grade 3 hypophosphatemia, 1 grade 4 febrile neutropenia). Fatigue, diarrhea, nausea, and anorexia were the most prevalent toxicities. No objective responses were documented, and four patients had stable disease for at least ten cycles. The long half-life (292.0 +/- 135.7 h), low clearance (0.045 +/- 0.038 l/h), and volume of distribution (14.3 +/- 5.9 l) observed for UCN-01 are consistent with prior UCN-01 data. There was a significant decrease in C(max) of APC, AUC of APC and SN-38, and AUC ratio of SN-38:irinotecan when comparing days 1 and 8 PK. CONCLUSIONS: APC and SN-38 exposure decreased when administered in combination with UCN-01. The MTD of the combination based on protocol criteria was defined as 70 mg/m(2) of UCN-01 on day 1 and 60 mg/m(2) of irinotecan on days 1 and 8 in a 21-day cycle.