Characterizing Opioid Prescribing Trends of Medical Oncologists From 2013 to 2019: Analysis From the Centers for Medicare & Medicaid Services Medicare Part D Prescribers Database.

PURPOSE: Opioid prescribing trends in medical oncology are poorly defined past 2017, the year after the CDC updated opioid prescription guidelines in noncancer settings. We aim to characterize pain management by medical oncologists by analyzing opioid and gabapentin prescribing trends from 2013 to 2019, identify physician-related factors associated with prescribing patterns, and assess whether CDC guidelines for nononcologic settings changed prescribing patterns. METHODS: The Centers for Medicare & Medicaid Services (CMS) Medicare Part D Prescribers-by Provider, CMS Medicare Part D Prescribers-by Provider and Drug, and CMS Medicare Physician National Downloadable files from 2013 to 2019 were merged by National Provider Identification. The database included physicians' sex, years of practice, regions, and practice settings. Multivariable binary logistic regression identified significant predictors of total opioid, long-acting opioid, and gabapentin prescriptions. RESULTS: Binary logistic regression modeling revealed no significant difference in mean daily total opioid prescriptions from 2013 to 2017. Daily opioid prescriptions by medical oncologists decreased significantly after 2017 (P < .001). Increased opioid prescribing was associated with physician male sex (P < .001), practicing over 10 years (P < .001), and practice in nonurban areas (P < .001). Opioid prescribing was greatest in the South and Midwest United States (P < .001). The same patterns were observed with total long-acting opioid prescriptions, whereas gabapentin prescribing increased from 2013 to 2019 (P < .001). CONCLUSION: Opioid prescriptions by medical oncologists decreased significantly from 2013 to 2019, but this decrease was most substantial from 2017 to 2019. These results may imply that the 2016 CDC guidelines influenced medical oncologists, particularly more junior physicians in urban settings, to manage chronic cancer pain with alternative therapies.

Disparities in lung cancer short- and long-term outcomes after surgery: Analysis from the national cancer database.

INTRODUCTION: Social determinants of health are particularly important in lung cancer epidemiology. Previous studies have primarily associated social determinants with long-term outcomes, such as survival, but fail to include short-term outcomes after surgery. The National Cancer Database (NCDB) was used to draw associations between social factors of patients with lung cancer and short-term post-surgical outcomes, while comparing them to prognostic factors, including stage at diagnosis and survival. METHODS: The 2004-17 NCDB was queried for patients with primary epithelial tumor, squamous cell carcinoma, or adenocarcinoma of the lung treated with curative intent. Linear, binary logistic, Kaplan-Meier, and Cox proportional hazards regression models were utilized. RESULTS: On logistic regression modeling, male gender, low income, lacking insurance, and facility in the central United States were associated with poor short-term outcomes (<0.05). Increased age, White race, and Black race were associated with increased length of hospital stay and mortality, but negatively correlated with readmission rates (<0.05). Medicare and Medicaid were associated with increased length of stay and mortality, respectively (<0.05). Similar patterns were observed for higher stage at diagnosis (<0.05). Hazard ratios were elevated with increased age, male gender, White race, lacking insurance, Medicaid, and facility in the central United States (<0.05). CONCLUSION: Many social factors previously associated with poor prognosis after lung cancer diagnosis are also associated with poor short-term outcomes after surgery. This study implies that healthcare providers treating lung cancer should proceed with care while aware that patients with the discussed social factors are predisposed to complicated recoveries.

Female authorship trends and the effect of COVID-19 on cataract and refractive surgery literature.

PURPOSE: To evaluate whether gender barriers persist specifically in the cataract and refractive surgery (CRS) literature. In addition, no literature exists investigating the long-term effect of COVID-19 on female authorship in ophthalmology past 2020. SETTING: Scopus 2015 to 2022. DESIGN: Retrospective data review. METHODS: Articles published in the Journal of Refractive Surgery and the Journal of Cataract & Refractive Surgery were recorded from January 2015 to February 2022 from Scopus. Articles with only 1 author or where gender could not be identified were excluded. The first author (FA) gender, senior author (SA) gender, affiliated country, type of literature, and number of citations were collected. Pearson chi-squared tests with phi coefficients and multivariate logistic regression were performed. RESULTS: 3153 articles were included in analysis. There were 910 works with female FAs and 648 with female SAs. Gender did not predict publishing in one journal over the other (P > .050). Women made up less than 30% of authorship of all types of literature, except for prospective/observational studies as FA (31.3%). Compared with before 2020, female FAs from 2020 onward were associated with increased retrospective analysis (phi = 0.072, P = .030) and letters/editorials (phi = 0.134, P < .001) but decreased case reports (phi = 0.087, P = .009) and "others" (phi = -0.164, P < .001). Similar associations were observed for female SAs. Females were more likely to publish in Asian countries. Female SAs predicted an increased likelihood of female FAs (odds ratio, 1.401, 95% CI, 1.165-1.684, P < .001). CONCLUSIONS: Gender disparities exist in authorship of the CRS literature. COVID-19 has altered the types of literature published by women, but men still publish most of all types of CRS research.

SWI/SNF complexes in hematological malignancies: biological implications and therapeutic opportunities.

Hematological malignancies are a highly heterogeneous group of diseases with varied molecular and phenotypical characteristics. SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complexes play significant roles in the regulation of gene expression, being essential for processes such as cell maintenance and differentiation in hematopoietic stem cells. Furthermore, alterations in SWI/SNF complex subunits, especially in ARID1A/1B/2, SMARCA2/4, and BCL7A, are highly recurrent across a wide variety of lymphoid and myeloid malignancies. Most genetic alterations cause a loss of function of the subunit, suggesting a tumor suppressor role. However, SWI/SNF subunits can also be required for tumor maintenance or even play an oncogenic role in certain disease contexts. The recurrent alterations of SWI/SNF subunits highlight not only the biological relevance of SWI/SNF complexes in hematological malignancies but also their clinical potential. In particular, increasing evidence has shown that mutations in SWI/SNF complex subunits confer resistance to several antineoplastic agents routinely used for the treatment of hematological malignancies. Furthermore, mutations in SWI/SNF subunits often create synthetic lethality relationships with other SWI/SNF or non-SWI/SNF proteins that could be exploited therapeutically. In conclusion, SWI/SNF complexes are recurrently altered in hematological malignancies and some SWI/SNF subunits may be essential for tumor maintenance. These alterations, as well as their synthetic lethal relationships with SWI/SNF and non-SWI/SNF proteins, may be pharmacologically exploited for the treatment of diverse hematological cancers.

Multi-omic alterations of the SWI/SNF complex define a clinical subgroup in lung adenocarcinoma.

SWI/SNF complexes are major targets of mutations in cancer. Here, we combined multiple "-omics" methods to assess SWI/SNF composition and aberrations in LUAD. Mutations in lung SWI/SNF subunits were highly recurrent in our LUAD cohort (41.4%), and over 70% of the mutations were predicted to have functional impact. Furthermore, SWI/SNF expression in LUAD suffered an overall repression that could not be explained exclusively by genetic alterations. Finally, SWI/SNF mutations were associated with poorer overall survival in TCGA-LUAD. We propose SWI/SNF-mutant LUAD as a separate clinical subgroup with practical implications.

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolved genetic interactions given the read-length limitations of next-generation sequencing platforms. This has hampered the direct observation of these genetic interactions that code for protein-protein interfaces with relevance in both drug and vaccine development. Here we overcome these technical limitations by developing a nanopore-based long-range viral sequencing pipeline that yields accurate single molecule sequences of circulating virions from clinical samples. We demonstrate its utility in observing the evolution of individual HIV Gag-Pol genomes in response to antiviral pressure. Our pipeline, called Multi-read Hairpin Mediated Error-correction Reaction (MrHAMER), yields >1000s of viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure and enables the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit.

Comprehensive Analysis of SWI/SNF Inactivation in Lung Adenocarcinoma Cell Models.

Mammalian SWI/SNF (SWitch/Sucrose Non-Fermentable) complexes are ATP-dependent chromatin remodelers whose subunits have emerged among the most frequently mutated genes in cancer. Studying SWI/SNF function in cancer cell line models has unveiled vulnerabilities in SWI/SNF-mutant tumors that can lead to the discovery of new therapeutic drugs. However, choosing an appropriate cancer cell line model for SWI/SNF functional studies can be challenging because SWI/SNF subunits are frequently altered in cancer by various mechanisms, including genetic alterations and post-transcriptional mechanisms. In this work, we combined genomic, transcriptomic, and proteomic approaches to study the mutational status and the expression levels of the SWI/SNF subunits in a panel of 38 lung adenocarcinoma (LUAD) cell lines. We found that the SWI/SNF complex was mutated in more than 76% of our LUAD cell lines and there was a high variability in the expression of the different SWI/SNF subunits. These results underline the importance of the SWI/SNF complex as a tumor suppressor in LUAD and the difficulties in defining altered and unaltered cell models for the SWI/SNF complex. These findings will assist researchers in choosing the most suitable cellular models for their studies of SWI/SNF to bring all of its potential to the development of novel therapeutic applications.

LncRNA-mRNA Co-Expression Analysis Identifies AL133346.1/CCN2 as Biomarkers in Pediatric B-Cell Acute Lymphoblastic Leukemia.

Pediatric acute B-cell lymphoblastic leukemia (B-ALL) constitutes a heterogeneous and aggressive neoplasia in which new targeted therapies are required. Long non-coding RNAs have recently emerged as promising disease-specific biomarkers for the clinic. Here, we identified pediatric B-ALL-specific lncRNAs and associated mRNAs by comparing the transcriptomic signatures of tumoral and non-tumoral samples. We identified 48 lncRNAs that were differentially expressed between pediatric B-ALL and healthy bone marrow samples. The most relevant lncRNA/mRNA pair was AL133346.1/CCN2 (previously known as RP11-69I8.3/CTGF), whose expression was positively correlated and increased in B-ALL samples. Their differential expression pattern and their strong correlation were validated in external B-ALL datasets (Therapeutically Applicable Research to Generate Effective Treatments, Cancer Cell Line Encyclopedia). Survival curve analysis demonstrated that patients with "high" expression levels of CCN2 had higher overall survival than those with "low" levels (p = 0.042), and this gene might be an independent prognostic biomarker in pediatric B-ALL. These findings provide one of the first detailed descriptions of lncRNA expression profiles in pediatric B-ALL and indicate that these potential biomarkers could help in the classification of leukemia subtypes and that CCN2 expression could predict the survival outcome of pediatric B-cell acute lymphoblastic leukemia patients.

LncRNA DLG2-AS1 as a Novel Biomarker in Lung Adenocarcinoma.

Long non-coding RNAs (lncRNAs) are a heterogeneous class of non-coding RNAs whose biological roles are still poorly understood. LncRNAs serve as gene expression regulators, frequently interacting with epigenetic factors to shape the outcomes of crucial biological processes, and playing roles in different pathologies including cancer. Over the last years, growing scientific evidence supports the key role of some lncRNAs in tumor development and proposes them as valuable biomarkers for the clinic. In this study, we aimed to characterize lncRNAs whose expression is altered in tumor samples from patients with lung adenocarcinoma (LUAD) compared to adjacent normal tissue samples. On an RT-qPCR survey of 90 cancer-related lncRNAs, we found one lncRNA, DLG2-AS1, which was consistently downregulated in 70 LUAD patients. To gain insight into its biological function, DLG2-AS1 was cloned and successfully re-expressed in LUAD cancer cell lines. We determined that DLG2-AS1 is not a cis-regulatory element of its overlapping gene DLG2, as their transcription levels were not correlated, nor did DLG2-AS1 restoration modify the expression of DLG2 protein. Furthermore, after generating a receiver operating curve (ROC) and calculating the area under curve (AUC), we found that DLG2-AS1 expression showed high sensitivity and specificity (AUC = 0.726) for the classification of LUAD and normal samples, determining its value as a potential lung cancer biomarker.

Magnetic couplings and magnetocaloric effect in the GdTX (T=Sc, Ti, Co, Fe; X=Si, Ge) compounds.

We compute the magnetocaloric effect (MCE) in the GdTX (T = Sc, Ti, Co, Fe; X = Si, Ge) compounds as a function of the temperature and the external magnetic field. To this end we use a density functional theory approach to calculate the exchange-coupling interactions between Gd3+ ions on each compound. We consider a simplified magnetic Hamiltonian and analyze the dependence of the exchange couplings on the transition metal T, the p-block element X, and the crystal structure (CeFeSi-type or CeScSi-type). The most significant effects are observed for the replacements Ti → Sc or Fe → Co which have an associated change in the parity of the electron number in the three dimensional level. These replacements lead to an antiferromagnetic contribution to the magnetic couplings that reduces the Curie temperature and can even lead to an antiferromagnetic ground state. We solve the magnetic models through mean field and Monte Carlo calculations and find large variations among compounds in the magnetic transition temperature and in the magnetocaloric effect, in agreement with the available experimental data. The magnetocaloric effect shows a universal behavior as a function of temperature and magnetic field in the ferromagnetic compounds after a scaling of the relevant energy scales by the Curie temperature T C.

VIPERdb: A Tool for Virus Research.

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.

Landau theory for magnetic and structural transitions in CeCo0.85Fe0.15Si.

We present a phenomenological analysis of the magnetoelastic properties of CeCo0.85Fe0.15Si at temperatures close to the Néel transition temperature T N. Using a Landau functional we provide a qualitative description of the thermal expansion, magnetostriction, magnetization and specific heat data. We show that the available experimental results (Correa et al 2016 J. Phys.: Condens. Matter 28 346003) are consistent with the presence of a structural transition at [Formula: see text] and a strong magnetoelastic coupling. The magnetoelastic coupling presents a Janus-faced effect: while the structural transition is shifted to higher temperatures as the magnetic field is increased, the resulting striction at low temperatures decreases. The strong magnetoelastic coupling and the proximity of the structural transition to the onset temperature for magnetic fluctuations, suggest that the transition could be an analogue of the tetragonal to orthorhombic observed in Fe-based pcnictides.

Structure based sequence analysis of viral and cellular protein assemblies.

It is well accepted that, in general, protein structural similarity is strongly related to the amino acid sequence identity. To analyze in great detail the correlation, distribution and variation levels of conserved residues in the protein structure, we analyzed all available high-resolution structural data of 5245 cellular complex-forming proteins and 293 spherical virus capsid proteins (VCPs). We categorized and compare them in terms of protein structural regions. In all cases, the buried core residues are the most conserved, followed by the residues at the protein-protein interfaces. The solvent-exposed surface shows greater sequence variations. Our results provide evidence that cellular monomers and VCPs could be two extremes in the quaternary structural space, with cellular dimers and oligomers in between. Moreover, based on statistical analysis, we detected a distinct group of icosahedral virus families whose capsid proteins seem to evolve much slower than the rest of the protein complexes analyzed in this work.

Nanogel surface coatings for improved single-molecule imaging substrates.

Surfaces that resist protein adsorption are important for many bioanalytical applications. Bovine serum albumin (BSA) coatings and multi-arm poly(ethylene glycol) (PEG) coatings display low levels of non-specific protein adsorption and have enabled highly quantitative single-molecule (SM) protein studies. Recently, a method was developed for coating a glass with PEG-BSA nanogels, a promising hybrid of these two low-background coatings. We characterized the nanogel coating to determine its suitability for SM protein experiments. SM adsorption counting revealed that nanogel-coated surfaces exhibit lower protein adsorption than covalently coupled BSA surfaces and monolayers of multi-arm PEG, so this surface displays one of the lowest degrees of protein adsorption yet observed. Additionally, the nanogel coating was resistant to DNA adsorption, underscoring the utility of the coating across a variety of SM experiments. The nanogel coating was found to be compatible with surfactants, whereas the BSA coating was not. Finally, applying the coating to a real-world study, we found that single ligand molecules could be tethered to this surface and detected with high sensitivity and specificity by a digital immunoassay. These results suggest that PEG-BSA nanogel coatings will be highly useful for the SM analysis of proteins.

Dynamical mean field theory with the density matrix renormalization group.

A new numerical method for the solution of the dynamical mean field theory's self-consistent equations is introduced. The method uses the density matrix renormalization group technique to solve the associated impurity problem. The new algorithm makes no a priori approximations and is only limited by the number of sites that can be considered. We obtain accurate estimates of the critical values of the metal-insulator transitions and provide evidence of substructure in the Hubbard bands of the correlated metal. With this algorithm, more complex models having a larger number of degrees of freedom can be considered and finite-size effects can be minimized.

In the privacy of their own homes: using the internet to assess racial bias.

Recent studies suggest that research participants show reduced distortion of their taboo attitudes and behaviors when they take part in Internet-based procedures from outside the laboratory. We explored whether such procedures would reduce distortion in the assessment of racial bias. In Study 1, White participants who completed the study in the laboratory evaluated Black targets more favorably than White targets. This unexpected "outgroup-favoring" pattern occurred in both pencil-and-paper and Internet versions of the study, showing that modality did not produce it; but when participants worked outside the laboratory via the Internet, this pattern disappeared. Study 2 replicated the above findings and further indicated that the reduced distortion in Internet-based studies was due to the removal of the experimenter rather than removing the participants from the laboratory environment. The implications of these findings for the study of controlled processes of prejudice and the nature of Internet-based social communication are discussed.