Integrating phylogenies into single-cell RNA sequencing analysis allows comparisons across species, genes, and cells.

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons evoke evolutionary histories, as depicted by phylogenetic trees, that define relationships between species, genes, and cells. This Essay considers each of these in turn, laying out challenges and solutions derived from a phylogenetic comparative approach and relating these solutions to previously proposed methods for the pairwise alignment of cellular dimensional maps. This Essay contends that species trees, gene trees, cell phylogenies, and cell lineages can all be reconciled as descriptions of the same concept-the tree of cellular life. By integrating phylogenetic approaches into scRNA-seq analyses, challenges for building informed comparisons across species can be overcome, and hypotheses about gene and cell evolution can be robustly tested.

Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores.

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.

Electrostatic particle ionization for suppressing air pollutants in cage-free layer facilities.

The increasing demand for cage-free (CF) poultry farming raises concern regarding air pollutant emissions in these housing systems. Previous studies have indicated that air pollutants such as particulate matter (PM) and ammonia (NH3) pose substantial risks to the health of birds and workers. This study aimed to evaluate the efficacy of electrostatic particle ionization (EPI) technology with different lengths of ion precipitators in reducing air pollutants and investigate the relationship between PM reduction and electricity consumption. Four identical CF rooms were utilized, each accommodating 175 hens of 77 wk of age (WOA). A Latin Square Design method was employed, with 4 treatment lengths: T1 = control (0 m), T2 = 12 ft (3.7 m), T3 = 24 ft (7.3 m), and T4 = 36 ft (11.0 m), where room and WOA are considered as blocking factors. Daily PM concentrations, temperature, and humidity measurements were conducted over 24 h, while NH3 levels, litter moisture content (LMC), and ventilation were measured twice a week in each treatment room. Statistical analysis involved ANOVA, and mean comparisons were performed using the Tukey HSD method with a significance level of P ≤ 0.05. This study found that the EPI system with longer wires reduced PM2.5 concentrations (P ≤ 0.01). Treatment T2, T3, and T4 led to reductions in PM2.5 by 12.1%, 19.3%, and 31.7%, respectively, and in small particle concentrations (particle size >0.5 µm) by 18.0%, 21.1%, and 32.4%, respectively. However, no significant differences were observed for PM10 and large particles (particle size >2.5 µm) (P < 0.10), though the data suggests potential reductions in PM10 (32.7%) and large particles (33.3%) by the T4 treatment. Similarly, there was no significant impact of treatment on NH3 reduction (P = 0.712), possibly due to low NH3 concentration (<2 ppm) and low LMC (<13%) among treatment rooms. Electricity consumption was significantly related to the length of the EPI system (P ≤ 0.01), with longer lengths leading to higher consumption rates. Overall, a longer-length EPI corona pipe is recommended for better air pollutant reduction in CF housing. Further research should focus on enhancing EPI technology, assessing cost-effectiveness, and exploring combinations with other PM reduction strategies.

Lipid-Encapsulated mRNAs Encoding Complex Fusion Proteins Potentiate Antitumor Immune Responses.

Lipid nanoparticle (LNP)-encapsulated mRNA has been used for in vivo production of several secreted protein classes, such as IgG, and has enabled the development of personalized vaccines in oncology. Establishing the feasibility of delivering complex multispecific modalities that require higher-order structures important for their function could help expand the use of mRNA/LNP biologic formulations. Here, we evaluated whether in vivo administration of mRNA/LNP formulations of SIRPα-Fc-CD40L and TIGIT-Fc-LIGHT could achieve oligomerization and extend exposure, on-target activity, and antitumor responses comparable with that of the corresponding recombinant fusion proteins. Intravenous infusion of the formulated LNP-encapsulated mRNAs led to rapid and sustained production of functional hexameric proteins in vivo, which increased the overall exposure relative to the recombinant protein controls by ∼28 to 140 fold over 96 hours. High concentrations of the mRNA-encoded proteins were also observed in secondary lymphoid organs and within implanted tumors, with protein concentrations in tumors up to 134-fold greater than with the recombinant protein controls 24 hours after treatment. In addition, SIRPα-Fc-CD40L and TIGIT-Fc-LIGHT mRNAs induced a greater increase in antigen-specific CD8+ T cells in the tumors. These mRNA/LNP formulations were well tolerated and led to a rapid increase in serum and intratumoral IL2, delayed tumor growth, extended survival, and outperformed the activities of benchmark mAb controls. Furthermore, the mRNA/LNPs demonstrated improved efficacy in combination with anti-PD-L1 relative to the recombinant fusion proteins. These data support the delivery of complex oligomeric biologics as mRNA/LNP formulations, where high therapeutic expression and exposure could translate into improved patient outcomes. SIGNIFICANCE: Lipid nanoparticle-encapsulated mRNA can efficiently encode complex fusion proteins encompassing immune checkpoint blockers and costimulators that functionally oligomerize in vivo with extended pharmacokinetics and durable exposure to induce potent antitumor immunity.

Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data.

The origin and evolution of cell types has emerged as a key topic in evolutionary biology. Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type evolution have largely been limited to pairwise comparisons because we lack approaches to build cell phylogenies using model-based approaches. Here we approach the challenges of applying explicit phylogenetic methods to single-cell data by using principal components as phylogenetic characters. We infer a cell phylogeny from a large, comparative single-cell dataset of eye cells from five distantly related mammals. Robust cell type clades enable us to provide a phylogenetic, rather than phenetic, definition of cell type, allowing us to forgo marker genes and phylogenetically classify cells by topology. We further observe evolutionary relationships between diverse vessel endothelia and identify the myelinating and non-myelinating Schwann cells as sister cell types. Finally, we examine principal component loadings and describe the gene expression dynamics underlying the function and identity of cell type clades that have been conserved across the five species. A cell phylogeny provides a rigorous framework towards investigating the evolutionary history of cells and will be critical to interpret comparative single-cell datasets that aim to ask fundamental evolutionary questions.

Normalizing need not be the norm: count-based math for analyzing single-cell data.

Counting transcripts of mRNA are a key method of observation in modern biology. With advances in counting transcripts in single cells (single-cell RNA sequencing or scRNA-seq), these data are routinely used to identify cells by their transcriptional profile, and to identify genes with differential cellular expression. Because the total number of transcripts counted per cell can vary for technical reasons, the first step of many commonly used scRNA-seq workflows is to normalize by sequencing depth, transforming counts into proportional abundances. The primary objective of this step is to reshape the data such that cells with similar biological proportions of transcripts end up with similar transformed measurements. But there is growing concern that normalization and other transformations result in unintended distortions that hinder both analyses and the interpretation of results. This has led to an intense focus on optimizing methods for normalization and transformation of scRNA-seq data. Here, we take an alternative approach, by avoiding normalization and transformation altogether. We abandon the use of distances to compare cells, and instead use a restricted algebra, motivated by measurement theory and abstract algebra, that preserves the count nature of the data. We demonstrate that this restricted algebra is sufficient to draw meaningful and practical comparisons of gene expression through the use of the dot product and other elementary operations. This approach sidesteps many of the problems with common transformations, and has the added benefit of being simpler and more intuitive. We implement our approach in the package countland, available in python and R.

Phylogenetic analyses of Reticulitermes (Blattodea: Rhinotermitidae) from California and other western states: multiple genes confirm undescribed species identified by cuticular hydrocarbons.

Subterranean termites in the genus Reticulitermes Holmgren 1913 are among the most economically important wood-destroying pests in the western United States. Yet, there remains uncertainty regarding the taxonomy and biology of the species in this genus. The 2 species described as having distributions in this region are the western subterranean termite, Reticulitermes hesperus Banks, and the arid land subterranean termite, Reticulitermes tibialis Banks. Taxonomic studies utilizing cuticular hydrocarbon (CHC) profiles, agonistic behavior, flight phenology, and mitochondrial DNA (mtDNA) suggested that R. hesperus is a species complex comprised of 2 or more sympatric, yet reproductively isolated species. To further delineate these taxa, we examined multiple genes from samples of Reticulitermes collected in the western United States. Alates collected after recent spring and fall mating flights, as well as previously collected workers, were subjected to CHC phenotyping and DNA sequence analyses that targeted mitochondrial cytochrome oxidase subunit II (COII), mitochondrial 16S rRNA, and nuclear Internal Transcribed Spacer 1 and 2 (ITS1 and 2). Phylogenetic analyses conducted also included published sequences of other putative western Reticulitermes species. Results suggest that at least 5 species of Reticulitermes may be present in California and that Reticulitermes in Arizona consistently group into multiple clades, including samples previously identified as R. tibialis in a sister clade. These analyses further support the species status of qualitatively different CHC phenotypes and that alates swarming in spring vs. fall are reproductively isolated species.

Tunable coupling in magnetic thin film heterostructures with a magnetic phase transition.

The magnetic properties of permalloy-based trilayers of the form Py0.8Cu0.2/Py0.4Cu0.6/Py/IrMn were studied as the spacer layer undergoes a paramagnetic to ferromagnetic phase transition. We find the coupling between the free Py0.8Cu0.2 layer and the exchange bias pinned Py to be strongly temperature-dependent: there is negligible coupling above the Curie temperature of the Py0.4Cu0.6 spacer layer, strong ferromagnetic coupling below that temperature, and a tunable coupling between these extremes. Polarized neutron reflectometry was used to measure the depth profile of the magnetic order in the system, allowing us to correlate the order parameter with the coupling strength. The thickness dependence shows that these are interface effects with an inverse relationship to thickness, and that there is a magnetic proximity effect that enhances the Curie temperature of the spacer layer with characteristic length scale of about 7 nm. As a demonstration of potential functionality of such a system, the structure is shown to spontaneously flip from the antiparallel to parallel magnetic configuration once the spacer layer has developed long-range magnetic order.

Semi-automated micro-computed tomography lung segmentation and analysis in mouse models.

Computed Tomography (CT) is a standard clinical tool utilized to diagnose known lung pathologies based on established grading methods. However, for preclinical trials and toxicity investigations in animal models, more comprehensive datasets are typically needed to determine discriminative features between experimental treatments, which oftentimes require analysis of multiple images and their associated differential quantification using manual segmentation methods. Furthermore, for manual segmentation of image data, three or more readers is the gold standard of analysis, but this requirement can be time-consuming and inefficient, depending on variability due to reader bias. In previous papers, microCT image manual segmentation was a valuable tool for assessment of lung pathology in several animal models; however, the manual segmentation approach and the commercial software used was typically a major rate-limiting step. To improve the efficiency, the semi-manual segmentation method was streamlined, and a semi-automated segmentation process was developed to produce:•Quantifiable segmentations: using manual and semi-automated analysis methods for assessing experimental injury and toxicity models,•Deterministic results and efficiency through automation in an unbiased and parameter free process, thereby reducing reader variance, user time, and increases throughput in data analysis,•Cost-Effectiveness: portable with low computational resource demand, based on a cross-platform open-source ImageJ program.

Electroencephalography in young onset dementia.

BACKGROUND: Young onset dementia (YOD) is a major diagnostic and management problem. METHODS: We set out to explore if electroencephalography (EEG) might be useful in the diagnosis of young onset Alzheimer's disease (YOAD) and young onset frontotemporal dementia (YOFTD). The ARTEMIS project is a 25-year prospective study of YOD based in Perth, Western Australia. 231 participants were included: YOAD: n = 103, YOFTD: n = 28, controls: n = 100. EEGs were performed prospectively, with 30-minute recording time for each subject, without knowledge of diagnosis or other diagnostic data. RESULTS: 80.9% of patients with YOD had abnormal EEGs (P < 0.00001). Slow wave changes were more frequent in YOAD that YOFTD (P < 0.00001), but no difference in the frequency of epileptiform activity (P = 0.32), with 38.8% of YOAD and 28.6% of YOFTD patients having epileptiform activity. Slow wave changes were more generalized in YOAD (P = 0.001). Slow wave changes and epileptiform activity were not sensitive to the diagnosis of YOD, but highly specific (97-99%). The absence of slow wave changes and epileptiform activity had a 100% negative predictive value and likelihood radio 0.14 and 0.62 respectively, meaning that those without slow wave changes or epileptiform activity had low probability of having YOD. No relationship was established between EEG findings and the patient's presenting problem. Eleven patients with YOAD developed seizures during the study, and only one with YOFTD. CONCLUSIONS: The EEG is highly specific for the diagnosis of YOD with the absence of slow wave changes and epileptiform phenomena making the diagnosis unlikely, with 100% negative predictive value and with low probability for the dementia diagnosis.

Shining a LIGHT on myeloid cell targeted immunotherapy.

Despite over a decade of clinical trials combining inhibition of emerging checkpoints with a PD-1/L1 inhibitor backbone, meaningful survival benefits have not been shown in PD-1/L1 inhibitor resistant or refractory solid tumours, particularly tumours dominated by a myelosuppressive microenvironment. Achieving durable anti-tumour immunity will therefore likely require combination of adaptive and innate immune stimulation, myeloid repolarisation, enhanced APC activation and antigen processing/presentation, lifting of the CD47/SIRPα (Cluster of Differentiation 47/signal regulatory protein alpha) 'do not eat me' signal, provision of an apoptotic 'pro-eat me' or 'find me' signal, and blockade of immune checkpoints. The importance of effectively targeting mLILRB2 and SIRPAyeloid cells to achieve improved response rates has recently been emphasised, given myeloid cells are abundant in the tumour microenvironment of most solid tumours. TNFSF14, or LIGHT, is a tumour necrosis superfamily ligand with a broad range of adaptive and innate immune activities, including (1) myeloid cell activation through Lymphotoxin Beta Receptor (LTßR), (2) T/NK (T cell and natural killer cell) induced anti-tumour immune activity through Herpes virus entry mediator (HVEM), (3) potentiation of proinflammatory cytokine/chemokine secretion through LTßR on tumour stromal cells, (4) direct induction of tumour cell apoptosis in vitro, and (5) the reorganisation of lymphatic tissue architecture, including within the tumour microenvironment (TME), by promoting high endothelial venule (HEV) formation and induction of tertiary lymphoid structures. LTBR (Lymphotoxin beta receptor) and HVEM rank highly amongst a range of costimulatory receptors in solid tumours, which raises interest in considering how LIGHT-mediated costimulation may be distinct from a growing list of immunotherapy targets which have failed to provide survival benefit as monotherapy or in combination with PD-1 inhibitors, particularly in the checkpoint acquired resistant setting.

Variability of microplastic loading and retention in four inland lakes in Minnesota, USA.

Microplastic pollution (plastic particles < 5 mm) has potentially harmful impacts on aquatic ecosystems. Understanding the factors that impact microplastic loading and distribution within aquatic ecosystems is crucial for assessing potential threats from microplastics. Here we examine the extent of microplastic pollution in the surface waters and sediments of four small inland lakes in Minnesota, USA that represent a range of human impacts as well as a variety of watershed and lake characteristics. Surface water particulates and benthic sediments were collected in the summers of 2019 and 2020 to examine the loading of microplastics into these lakes and their distribution throughout the ecosystems. Lower size cut offs were set at 330 µm for surface water particulate samples and 250 µm for sediment samples. Watershed to surface area ratio (WS:SA) and urban development were the most influential factors on microplastic loading. Surface water microplastic concentrations ranged from 27,000 microplastics km-2 in Elk Lake (small WS:SA and minimally developed) to 152,000 microplastics km-2 in White Iron Lake (large WS:SA and low development). Concentrations in benthic sediments ranged from 30 microplastics kg-1 dry sediment in White Iron Lake (forested watershed) to 270 microplastics kg-1 dry sediment in Peltier Lake (urbanized watershed) and were not directly correlated to surface water concentrations. Results from this study highlight the characteristics of small lakes that influence spatial and temporal variability in microplastic loading, retention, and deposition of microplastics to sediments. Further, this study demonstrates the difficulties of accurately predicting microplastic loading and the importance of comprehensive sampling to account for the variability of microplastic loading and distribution in smaller inland lakes.

The origins and functional effects of postzygotic mutations throughout the human life span.

Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remain unclear. To study the origins and functional consequences of PZMs, we generated a multitissue atlas of PZMs spanning 54 tissue and cell types from 948 donors. Nearly half the variation in mutation burden among tissue samples can be explained by measured technical and biological effects, and 9% can be attributed to donor-specific effects. Through phylogenetic reconstruction of PZMs, we found that their type and predicted functional impact vary during prenatal development, across tissues, and through the germ cell life cycle. Thus, methods for interpreting effects across the body and the life span are needed to fully understand the consequences of genetic variants.

Optimized Atlas-Based Auto-Segmentation of Bony Structures from Whole-Body Computed Tomography.

PURPOSE: To develop and test a method for fully automated segmentation of bony structures from whole-body computed tomography (CT) and evaluate its performance compared with manual segmentation. METHODS AND MATERIALS: We developed a workflow for automatic whole-body bone segmentation using atlas-based segmentation (ABS) method with a postprocessing module (ABSPP) in MIM MAESTRO software. Fifty-two CT scans comprised the training set to build the atlas library, and 29 CT scans comprised the test set. To validate the workflow, we compared Dice similarity coefficient (DSC), mean distance to agreement, and relative volume errors between ABSPP and ABS with no postprocessing (ABSNPP) with manual segmentation as the reference (gold standard). RESULTS: The ABSPP method resulted in significantly improved segmentation accuracy (DSC range, 0.85-0.98) compared with the ABSNPP method (DSC range, 0.55-0.87; P < .001). Mean distance to agreement results also indicated high agreement between ABSPP and manual reference delineations (range, 0.11-1.56 mm), which was significantly improved compared with ABSNPP (range, 1.00-2.34 mm) for the majority of tested bony structures. Relative volume errors were also significantly lower for ABSPP compared with ABSNPP for most bony structures. CONCLUSIONS: We developed a fully automated MIM workflow for bony structure segmentation from whole-body CT, which exhibited high accuracy compared with manual delineation. The integrated postprocessing module significantly improved workflow performance.

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.

Outcomes from a 3-fraction high-dose-rate brachytherapy regimen for patients with cervical cancer.

PURPOSE: To estimate local control, survival, and toxicity associated with a 3-fraction (3F) image-guided brachytherapy (IGBT) regimen compared to longer fraction (LF) for cervical cancer. METHODS: 150 patients treated between 2015-2020 with 3F (24Gy in 3 fractions) or LF (28...30 Gy in 4-5 fractions) were reviewed. The primary outcome was 2-year local failure. We compared overall survival (OS), disease-free survival (DFS), hospitalizations, and toxicity. RESULTS: There were 32 patients in the 3F group and 118 in the LF group, with a median follow up of 22 months. The 3F had worse performance status (p = 0.01) but otherwise similar characteristics. The 2-year local failure rate was 3.6% (95% CI 0%, 10.6%) for 3F, and 7.5% (95% CI 2.4%, 12.6%) for LF. The univariable hazard ratio (HR) for local failure for 3F was 0.43 (0.05, 3.43; p = 0.43). Moreover, 2 of 32 (6.3%) 3F patients experienced Grade ...3 toxicity compared to 7 of 118 (5.9%) LF patients (p = 1.0), with no difference in hospitalization within 2 years (p = 0.66) and no treatment-related deaths. CONCLUSIONS: Local control was excellent, with long term survival and toxicity similar between the groups. These findings support consideration of 3F.

Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic.

OBJECTIVES: Molecular epidemiology is a powerful tool to characterize HIV epidemics and prioritize public health interventions. Typically, HIV clusters are assumed to have uniform patterns over time. We hypothesized that assessment of cluster evolution would reveal distinct cluster behavior, possibly improving molecular epidemic characterization, towards disrupting HIV transmission. DESIGN: Retrospective cohort. METHODS: Annual phylogenies were inferred by cumulative aggregation of all available HIV-1 pol sequences of individuals with HIV-1 in Rhode Island (RI) between 1990 and 2020, representing a statewide epidemic. Molecular clusters were detected in annual phylogenies by strict and relaxed cluster definition criteria, and the impact of annual newly-diagnosed HIV-1 cases to the structure of individual clusters was examined over time. RESULTS: Of 2153 individuals, 31% (strict criteria) - 47% (relaxed criteria) clustered. Longitudinal tracking of individual clusters identified three cluster types: normal, semi-normal and abnormal. Normal clusters (83-87% of all identified clusters) showed predicted growing/plateauing dynamics, with approximately three-fold higher growth rates in large (15-18%) vs. small (∼5%) clusters. Semi-normal clusters (1-2% of all clusters) temporarily fluctuated in size and composition. Abnormal clusters (11-16% of all clusters) demonstrated collapses and re-arrangements over time. Borderline values of cluster-defining parameters explained dynamics of non-normal clusters. CONCLUSIONS: Comprehensive tracing of molecular HIV clusters over time in a statewide epidemic identified distinct cluster types, likely missed in cross-sectional analyses, demonstrating that not all clusters are equal. This knowledge challenges current perceptions of consistent cluster behavior over time and could improve molecular surveillance of local HIV epidemics to better inform public health strategies.

The evolution of ovary-biased gene expression in Hawaiian Drosophila.

With detailed data on gene expression accessible from an increasingly broad array of species, we can test the extent to which our developmental genetic knowledge from model organisms predicts expression patterns and variation across species. But to know when differences in gene expression across species are significant, we first need to know how much evolutionary variation in gene expression we expect to observe. Here we provide an answer by analyzing RNAseq data across twelve species of Hawaiian Drosophilidae flies, focusing on gene expression differences between the ovary and other tissues. We show that over evolutionary time, there exists a cohort of ovary specific genes that is stable and that largely corresponds to described expression patterns from laboratory model Drosophila species. Our results also provide a demonstration of the prediction that, as phylogenetic distance increases, variation between species overwhelms variation between tissue types. Using ancestral state reconstruction of expression, we describe the distribution of evolutionary changes in tissue-biased expression, and use this to identify gains and losses of ovary-biased expression across these twelve species. We then use this distribution to calculate the evolutionary correlation in expression changes between genes, and demonstrate that genes with known interactions in D. melanogaster are significantly more correlated in their evolution than genes with no or unknown interactions. Finally, we use this correlation matrix to infer new networks of genes that share evolutionary trajectories, and we present these results as a dataset of new testable hypotheses about genetic roles and interactions in the function and evolution of the Drosophila ovary.

Underutilization of brachytherapy for cervical cancer in the United States.

Brachytherapy is a critical component of the definitive management of cervical cancer and allows for the safe delivery of about half of the total effective radiation dose needed for optimal outcomes. Moreover, the dose distribution of brachytherapy is highly conformal, allowing for a therapeutic index currently unmatched by alternative techniques. However, a modern brachytherapy program requires special equipment, infrastructure, and procedural expertise. Unfortunately, multiple lines of evidence suggest that brachytherapy is currently underutilized in the United States. In this review, we examine the importance of brachytherapy, contemporary recommendations, and avenues for growth.

Quantitative prediction of aspiration risk in head and neck cancer patients treated with radiation therapy.

OBJECTIVE: To determine characteristics most strongly associated with risk for aspiration events among head and neck cancer (HNC) patients undergoing curative intent treatment. MATERIALS AND METHODS: This was a retrospective, cross-sectional study of 106 patients with previously untreated HNC who received definitive or postoperative radiation therapy (RT) +/- systemic therapy with curative intent. Patients who received post-treatment videofluoroscopic swallow study (VFSS) between 2018-2021 were included. Using ordinal multivariable logistic regression, we modeled the effects of age (>60 years vs. ≤60 years), sex, body mass index (BMI) (>20 kg/m2 vs. ≤20 kg/m2), American Joint Committee on Cancer 8th edition stage (I-II vs. III-IVB), treatment with cisplatin (vs. other or no systemic therapy), post-operative status, primary site (oral cavity vs. P16+ oropharynx vs. P16- Mucosal Site vs. other), and quantitative VFSS measures on Penetration-Aspiration Scale (PAS) score. RESULTS AND CONCLUSION: On ordinal multivariable logistic regression, age >60 years (odds ratio (OR): 3.91, 95% confidence interval (CI): 1.29, 11.9), advanced stage (stage III-IVB) (OR: 3.13, 95% CI: 1.23, 7.79), pharyngeal constriction ratio (PCR) >0.25 (OR: 3.65, 95% CI: 1.14, 11.7), and bolus clearance ratio (BCR) > 0.10 (OR: 3.42, 95% CI: 1.20, 9.75) were found to be significant risk factors for higher PAS scores. Patients with ≥ 2 pre-treatment risk factors had statistically significant increased risk for post-treatment aspiration (OR 2.52, 95% CI: 1.31, 4.86) on ordinal logistic regression. This model could be useful to direct high-risk patients toward interventions designed to reduce risk of aspiration events.