Iron Supplementation Increases Tumor Burden and Alters Protein Expression in a Mouse Model of Human Intestinal Cancer

Iron supplements are widely consumed. However, excess iron may accelerate intestinal tumorigenesis. To determine the effect of excess iron on intestinal tumor burden and protein expression changes between tumor and normal tissues, ApcMin/+ mice were fed control (adequate) and excess iron (45 and 450 mg iron/kg diet, respectively; n = 9/group) for 10 wk. Tumor burden was measured, and two-dimensional fluorescence difference gel electrophoresis was used to identify differentially expressed proteins in tumor and normal intestinal tissues. There was a significant increase (78.3%; p ≤ 0.05) in intestinal tumor burden (mm2/cm) with excess iron at wk 10. Of 980 analyzed protein spots, 69 differentially expressed (p ≤ 0.05) protein isoforms were identified, representing 55 genes. Of the isoforms, 56 differed (p ≤ 0.05) between tumor vs. normal tissues from the adequate iron group and 23 differed (p ≤ 0.05) between tumors from the adequate vs. excess iron. Differentially expressed proteins include those involved in cell integrity and adaptive response to reactive oxygen species (including, by gene ID: ANPEP, DPP7, ITGB1, PSMA1 HSPA5). Biochemical pathway analysis found that iron supplementation modulated four highly significant (p ≤ 0.05) functional networks. These findings enhance our understanding of interplay between dietary iron and intestinal tumorigenesis and may help develop more specific dietary guidelines regarding trace element intake.

Effect of Polymer Gel Elasticity on Complex Coacervate Phase Behavior

Gels are key materials in biological systems such as tissues and may control biocondensate formation and structure. To further understand the effects of elastic environments on biomacromolecular assembly, we have investigated the phase behavior and radii of complex coacervate droplets in polyacrylamide (PAM) networks as a function of gel modulus. Poly-l-lysine (PLL) and sodium hyaluronate (HA) complex coacervate phases were prepared in PAM gels with moduli varying from 0.035 to 15.0 kPa. The size of the complex coacervate droplets is reported from bright-field microscopy and confocal fluorescence microscopy. Overall, the complex coacervate droplet volume decreases inversely with the modulus. Fluorescence microscopy is also used to determine the phase behavior and concentration of fluorescently tagged HA in the complex coacervate phases as a function of ionic strength (100-270 mM). We find that the critical ionic strength and complex coacervate stability are nonmonotonic as a function of the network modulus and that the local gel concentration can be used to control phase behavior and complex coacervate droplet size scale. By understanding how elastic environments influence simple electrostatic assembly, we can further understand how biomacromolecules exist in complex, crowded, and elastic cellular environments.

Preliminary content and construct validity of a new model to differentiate research skills from evidence-based practice skills: Core, Evidence Application, Research (CEAR) Model

BACKGROUND

Research is the scientific basis for the profession of dietetics, as it must be located and applied in evidence-based practice (EBP). EBP is often presented as a foundational skill for research. CEAR - Core, Evidence Application, Research - is a newly proposed model that separates Research and Evidence Application skills into distinct domains, jointly supported by a set of Core skills, thus acknowledging that education and advancement in one domain neither requires nor precipitates education and advancement in the other. The goal was to investigate the content and construct validity of the new CEAR Model.

METHODS

A cross-sectional online survey of randomly selected dietitians in the United States was used to collect CEAR domain scores, validated measures of research or EBP skills and self-reported characteristics. Exploratory factor analysis, Cronbach's α and Pearson correlation between various tools and CEAR domains were used to assess validity and reliability. Analysis of variance (ANOVA) and multiple linear regression between CEAR domains and participant characteristics were used to assess convergent and divergent validity.

RESULTS

One hundred and fifty-four responses with a valid CEAR score were received and led to a three-factor solution, supporting the theorised differentiation of research from evidence application skills (content validity). Internal reliability for the CEAR Model overall and for each domain was high. The hypothesised correlations between existing research or EBP measurement tools and the relevant CEAR domains were found (construct validity). Known groups analysis demonstrated the expected differences in CEAR domain scores based on participant characteristics.

CONCLUSIONS

The CEAR Model demonstrates preliminary validity and internal reliability. It adds to the current literature by acknowledging the separateness of evidence application skills from research skills.

Human alveolar macrophages display marked hypo-responsiveness to IFN-γ in both proteomic and gene expression analysis

Alveolar macrophages (AM) perform a primary defense mechanism in the lung through phagocytosis of inhaled particles and microorganisms. AM are known to be relatively immunosuppressive consistent with the aim to limit alveolar inflammation and maintain effective gas exchange in the face of these constant challenges. How AM respond to T cell derived cytokine signals, which are critical to the defense against inhaled pathogens, is less well understood. For example, successful containment of Mycobacterium tuberculosis (Mtb) in lung macrophages is highly dependent on IFN-γ secreted by Th-1 lymphocytes, however, the proteomic IFN-γ response profile in AM remains mostly unknown. In this study, we measured IFN-γ induced protein abundance changes in human AM and autologous blood monocytes (MN). AM cells were activated by IFN-γ stimulation resulting in STAT1 phosphorylation and production of MIG/CXCL9 chemokine. However, the global proteomic response to IFN-γ in AM was dramatically limited in comparison to that of MN (9 AM vs 89 MN differentially abundant proteins). AM hypo-responsiveness was not explained by reduced JAK-STAT1 signaling nor increased SOCS1 expression. These findings suggest that AM have a tightly regulated response to IFN-γ which may prevent excessive pulmonary inflammation but may also provide a niche for the initial survival and growth of Mtb and other intracellular pathogens in the lung.

magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing

Recently, novel biotechnologies to quantify RNA modifications became an increasingly popular choice for researchers who study epitranscriptome. When studying RNA methylations such as N6-methyladenosine (m6A), researchers need to make several decisions in its experimental design, especially the sample size and a proper statistical power. Due to the complexity and high-throughput nature of m6A sequencing measurements, methods for power calculation and study design are still currently unavailable. In this work, we propose a statistical power assessment tool, magpie, for power calculation and experimental design for epitranscriptome studies using m6A sequencing data. Our simulation-based power assessment tool will borrow information from real pilot data, and inspect various influential factors including sample size, sequencing depth, effect size, and basal expression ranges. We integrate two modules in magpie: (i) a flexible and realistic simulator module to synthesize m6A sequencing data based on real data; and (ii) a power assessment module to examine a set of comprehensive evaluation metrics.

Chemically Stable Styrenic Electrospun Membranes with Tailorable Surface Chemistry

Membranes with tailorable surface chemistry have applications in a wide range of industries. Synthesizing membranes from poly(chloromethyl styrene) directly incorporates an alkyl halide surface-bound initiator which can be used to install functional groups via SN2 chemistry or graft polymerization techniques. In this work, poly(chloromethyl styrene) membranes were synthesized through electrospinning. After fabrication, membranes were crosslinked with a diamine, and the chemical resistance of the membranes was evaluated by exposure to 10 M nitric acid, ethanol, or tetrahydrofuran for 24 h. The resulting membranes had diameters on the order of 2-5 microns, porosities of >80%, and permeance on the order of 10,000 L/m2/h/bar. Crosslinking the membranes generally increased the chemical stability. The degree of crosslinking was approximated using elemental analysis for nitrogen and ranged from 0.5 to 0.9 N%. The poly(chloromethyl styrene) membrane with the highest degree of crosslinking did not dissolve in THF after 24 h and retained its high permeance after solvent exposure. The presented chemically resistant membranes can serve as a platform technology due to their versatile surface chemistry and can be used in membrane manufacturing techniques that require the membrane to be contacted with organic solvents or monomers. They can also serve as a platform for separations that are performed in strong acids.

An analysis of the impact of annual cancer genetic testing guideline updates on a past patient population

Germline genetic testing for cancer predisposition genes has become an essential component of cancer treatment and risk reduction. The National Comprehensive Cancer Network (NCCN) releases annual genetic testing guidelines that identify characteristics of patients that could be affected by a hereditary cancer syndrome. These guidelines have broadened over time and the implications for past patients of cancer genetics clinics are not well understood. This study is a retrospective chart review aimed at determining the percentage and characteristics of past patients that meet updated NCCN guidelines (Breast, Ovarian, and Pancreas [BOP] v1.2022 and Colorectal [CRC] v1.2021), patients that attended a follow-up appointment, and patients who went on to receive genetic testing. Clinical data and characteristics were compared between the study population as a whole and the cohort of patients that met updated NCCN guidelines BOP v1.2022 and CRC v1.2021. The study population consisted of 280 patients with 76 (27.1%) patients meeting updated NCCN guidelines BOP v1.2022 and CRC v1.2021. The year of initial cancer genetic counseling appointment was statistically significant (p = 0.023) with patients more likely to meet NCCN guidelines BOP v1.2022 and CRC v1.2021 with earlier initial cancer genetic counseling appointments. In the cohort that met updated NCCN guidelines BOP v1.2022 and CRC v1.2021, the most common reason was a change in the NCCN guidelines (BOP or CRC) (54/76, 71.1%) with triple-negative breast cancer diagnosed at any age being the most impactful guideline change (19/54, 35.2%). Twenty-one patients attended a follow-up appointment (7.5%) and of those that received genetic testing (17/21, 81%) most received negative results (13/17, 61.9%), with one pathogenic, low penetrance result (1/17, 5.9%, CHEK2 p.I157T). Provider-initiated follow-up was attributed to most follow-up appointments (16/21, 76.2%) implying patients do not tend to follow-up on their own. Education to non-genetics providers as well as targeted implementation of follow-up protocols possibly managed by genetic counseling assistants and utilizing electronic medical record (EMR) patient messaging could lead to improved patient follow-up.

Evaluating Dual-Targeted ECO/siRNA Nanoparticles against an Oncogenic lncRNA for Triple Negative Breast Cancer Therapy with Magnetic Resonance Molecular Imaging

Differentiation antagonizing noncoding RNA (DANCR) is recognized as an oncogenic long noncoding RNA (lncRNA) overexpressed in triple negative breast cancer (TNBC). We showed in a previous study that RNAi with targeted multifunctional ionizable lipid ECO/siRNA nanoparticles was effective to regulate this undruggable target for effective treatment of TNBC. In this study, we developed dual-targeted ECO/siDANCR nanoparticles by targeting a tumor extracellular matrix oncoprotein, extradomain B fibronectin (EDB-FN), and integrins overexpressed on cancer cells for enhanced delivery of siDANCR. The treatment of Hs578T TNBC cells and MCF-7 estrogen receptor-positive cells in vitro resulted in significant down-regulation of DANCR and EDB-FN and suppressed invasion and 3D spheroid formation of the cells. Magnetic resonance molecular imaging (MRMI) with an EDB-FN-targeted contrast agent, MT218, was used to noninvasively evaluate tumor response to treatment with the targeted ECO/siDANCR nanoparticles in female nude mice bearing orthotopic Hs578T and MCF-7 xenografts. MRMI with MT218 was effective to differentiate between aggressive TNBC with high DANCR and EDB-FN expression and ER+ MCF-7 tumors with low expression of the targets. MRMI showed that the dual-targeted ECO/siDANCR nanoparticles resulted in more significant inhibition of tumor growth in both models than the controls and significantly reduced EDB-FN expression in the TNBC tumors. The combination of MRMI and dual-targeted ECO/siDANCR nanoparticles is a promising approach for image-guided treatment of TNBC by regulating the onco-lncRNA.

A social network analysis model approach to understand tuberculosis transmission in remote rural Madagascar

BACKGROUND

Quality surveillance data used to build tuberculosis (TB) transmission models are frequently unavailable and may overlook community intrinsic dynamics that impact TB transmission. Social network analysis (SNA) generates data on hyperlocal social-demographic structures that contribute to disease transmission.

METHODS

We collected social contact data in five villages and built SNA-informed village-specific stochastic TB transmission models in remote Madagascar. A name-generator approach was used to elicit individual contact networks. Recruitment included confirmed TB patients, followed by snowball sampling of named contacts. Egocentric network data were aggregated into village-level networks. Network- and individual-level characteristics determining contact formation and structure were identified by fitting an exponential random graph model (ERGM), which formed the basis of the contact structure and model dynamics. Models were calibrated and used to evaluate WHO-recommended interventions and community resiliency to foreign TB introduction.

RESULTS

Inter- and intra-village SNA showed variable degrees of interconnectivity, with transitivity (individual clustering) values of 0.16, 0.29, and 0.43. Active case finding and treatment yielded 67%-79% reduction in active TB disease prevalence and a 75% reduction in TB mortality in all village networks. Following hypothetical TB elimination and without specific interventions, networks A and B showed resilience to both active and latent TB reintroduction, while Network C, the village network with the highest transitivity, lacked resiliency to reintroduction and generated a TB prevalence of 2% and a TB mortality rate of 7.3% after introduction of one new contagious infection post hypothetical elimination.

CONCLUSION

In remote Madagascar, SNA-informed models suggest that WHO-recommended interventions reduce TB disease (active TB) prevalence and mortality while TB infection (latent TB) burden remains high. Communities' resiliency to TB introduction decreases as their interconnectivity increases. "Top down" population level TB models would most likely miss this difference between small communities. SNA bridges large-scale population-based and hyper focused community-level TB modeling.

Association of Social Determinants of Health and Clinical Factors with Postpartum Hospital Readmissions among Nulliparous Individuals

OBJECTIVE

Prior data suggest that there are racial and ethnic disparities in postpartum readmission among individuals, especially among those with hypertensive disorders of pregnancy. Existing reports commonly lack granular information on social determinants of health. The objective of this study was to investigate factors associated with postpartum readmission for individuals and address whether such risk factors differed by whether an individual had an antecedent diagnosis of a hypertensive disorder of pregnancy (HDP).

STUDY DESIGN

This is a secondary analysis of a large, multicenter prospective cohort study of 10,038 nulliparous participants. The primary outcome of this analysis was postpartum readmission. A priori, participants were analyzed separately based on whether they had HDP. Participant characteristics previously associated with a greater risk of perinatal morbidity or readmission (including social determinants of health, preexisting and chronic comorbidities, and intrapartum characteristics) were compared with bivariable analyses and retained in multivariable models if p < 0.05. Social determinants of health evaluated in this analysis included insurance status, self-identified race and ethnicity (as a proxy for structural racism), income, marital status, primary language, and educational attainment.

RESULTS

Of 9,457 participants eligible for inclusion, 1.7% (n = 165) were readmitted following initial hospital discharge. A higher proportion of individuals with HDP were readmitted compared with individuals without HDP (3.4 vs 1.3%, p < 0.001). Among participants without HDP, the only factors associated with postpartum readmission were chorioamnionitis and cesarean delivery. Among participants with HDP, gestational diabetes and postpartum hemorrhage requiring transfusion were associated with postpartum readmission. While the number of postpartum readmissions included in our analysis was relatively small, social determinants of health that we examined were not associated with postpartum readmission for either group.

CONCLUSION

In this diverse cohort of nulliparous pregnant individuals, there was a higher frequency of postpartum readmission among participants with HDP. Preexisting comorbidity and intrapartum complications were associated with postpartum readmission among this population engaged in a longitudinal study.

KEY POINTS

· Non-HDP patients had higher odds of PPR with chorioamnionitis or cesarean.. · HDP patients had higher odds of PPR if they had GDM or PPH.. · Characterizing PPR may identify and highlight modifiable factors..

Rifapentine With and Without Moxifloxacin for Pulmonary Tuberculosis in People With Human Immunodeficiency Virus (S31/A5349)

BACKGROUND

Tuberculosis (TB) Trials Consortium Study 31/AIDS Clinical Trials Group A5349, an international randomized open-label phase 3 noninferiority trial showed that a 4-month daily regimen substituting rifapentine for rifampin and moxifloxacin for ethambutol had noninferior efficacy and was safe for the treatment of drug-susceptible pulmonary TB (DS-PTB) compared with the standard 6-month regimen. We explored results among the prespecified subgroup of people with human immunodeficiency virus (HIV) (PWH).

METHODS

PWH and CD4+ counts ≥100 cells/μL were eligible if they were receiving or about to initiate efavirenz-based antiretroviral therapy (ART). Primary endpoints of TB disease-free survival 12 months after randomization (efficacy) and ≥ grade 3 adverse events (AEs) on treatment (safety) were compared, using a 6.6% noninferiority margin for efficacy. Randomization was stratified by site, pulmonary cavitation, and HIV status. PWH were enrolled in a staged fashion to support cautious evaluation of drug-drug interactions between rifapentine and efavirenz.

RESULTS

A total of 2516 participants from 13 countries in sub-Saharan Africa, Asia, and the Americas were enrolled. Among 194 (8%) microbiologically eligible PWH, the median CD4+ count was 344 cells/μL (interquartile range: 223-455). The rifapentine-moxifloxacin regimen was noninferior to control (absolute difference in unfavorable outcomes -7.4%; 95% confidence interval [CI] -20.8% to 6.0%); the rifapentine regimen was not noninferior to control (+7.5% [95% CI, -7.3% to +22.4%]). Fewer AEs were reported in rifapentine-based regimens (15%) than the control regimen (21%).

CONCLUSIONS

In people with HIV-associated DS-PTB with CD4+ counts ≥100 cells/μL on efavirenz-based ART, the 4-month daily rifapentine-moxifloxacin regimen was noninferior to the 6-month control regimen and was safe.

CLINICAL TRIALS REGISTRATION

NCT02410772.

Critical behavior and the Kibble-Zurek mechanism in a musical phase transition

We investigate the critical phenomena emerging from a statistical mechanics model of musical harmony on a three-dimensional (3D) lattice, and the resulting structure of the ordered phase. In this model, each lattice site represents a tone, with nearest neighbors interacting via the perception of dissonance between them. With dissonance assumed to be an octave-wise periodic function of pitch difference, this model is a 3D XY system with the same symmetry and dimensionality as superfluid helium and models of the cosmological axion field. We use numerical simulation to observe a phase transition from disordered sound to ordered arrangements of musical pitches as a parameter analogous to the temperature is quenched towards zero. We observe the divergence of correlation length and relaxation time at the phase boundary, consistent with the critical exponents in similar systems. Furthermore, the quenched low-temperature phase of these systems displays topological defects in the form of vortex strings that thread throughout the system volume. We observe the formation of these vortex strings in accordance with the Kibble-Zurek mechanism, and discuss the structure of these vortex strings in the context of the theory of musical harmony, finding both similarities to established music theory, and uncovering new avenues to explore.

Beyond Competence: Efficiency in American Biomedicine

"Competence" is a longstanding value of American biomedicine. One underidentified corollary of competence is efficiency: at once a manifestation of competence, a challenge to competence, and a virtue in its own right. We will explore the social construction of efficiency in US undergraduate medical education through an analysis of its sociocultural and technological landscapes. We present qualitative data from two allopathic medical school field sites in the Midwestern United States, where medical students' careful selection of certain learning resources and overall perspectives on the curriculum underscore their focus on efficiency and pragmatic approaches to knowledge. In the discussion, we consider the ethical implications of physician efficiency, as well as future trajectories for the study of efficiency in the medical social sciences, bioethics, and medical education. We posit that efficiency is at the theoretical heart of US medical practice and education: a finding that has wide-reaching implications for how researchers conceptualize the enterprise of biomedicine across cultural contexts and interpret the lived experiences of physicians, medical students, and other clinicians.

Deterioration of Glycemic Control in Youth-Onset Type 2 Diabetes: What Are the Early and Late Predictors?

OBJECTIVE

We examined predictors of early and late loss of glycemic control in individuals with youth-onset type 2 diabetes, as well as predictors of short-term deterioration in youth from the Treatment Options for type 2 Diabetes in Adolescents and Youth (TODAY) study.

METHODS

Demographic, physical, and biochemical measures at baseline and 48 months, and change over time, were examined in 584 participants separated into those with loss of glycemic control (sustained HbA1c ≥ 8%) before 48 months or at 48 months or later, and those who remained in control until the end of the study (median 6.8 years). Univariate and multivariate models, and receiver operating characteristic curve analyses were performed.

RESULTS

Approximately 45% of youth remained in control at 48 months; of these, 30% subsequently lost glycemic control prior to the end of follow-up. Predictors of early loss of glycemic control included baseline HbA1c, C-peptide index, oral disposition index, proinsulin, and proinsulin to insulin ratio. Predictors of late loss included baseline measures of insulin secretion and change in HbA1c and insulin processing at 48 months. A baseline HbA1c cutoff of ≥ 6.2% was optimally predictive of loss of glycemic control at any time, while an absolute rise in HbA1c > 0.5% related to loss of glycemic control within 3 to 6 months.

CONCLUSION

This analysis demonstrates that youth with type 2 diabetes at risk for loss of glycemic control, including impending rapid deterioration, can be identified using available clinical measures, allowing for closer monitoring of at-risk youth, and facilitating the design of research on better therapeutic options.

Recruitment of the CoREST transcription repressor complexes by Nerve Growth factor IB-like receptor (Nurr1/NR4A2) mediates silencing of HIV in microglial cells

Human immune deficiency virus (HIV) infection in the brain leads to chronic neuroinflammation due to the production of pro-inflammatory cytokines, which in turn promotes HIV transcription in infected microglial cells. However, powerful counteracting silencing mechanisms in microglial cells result in the rapid shutdown of HIV expression after viral reactivation to limit neuronal damage. Here we investigated whether the Nerve Growth Factor IB-like nuclear receptor Nurr1 (NR4A2), which is a repressor of inflammation in the brain, acts directly to restrict HIV expression. HIV silencing following activation by TNF-α, or a variety of toll-like receptor (TLR) agonists, in both immortalized human microglial cells (hμglia) and induced pluripotent stem cells (iPSC)-derived human microglial cells (iMG) was enhanced by Nurr1 agonists. Similarly, overexpression of Nurr1 led to viral suppression, while conversely, knock down (KD) of endogenous Nurr1 blocked HIV silencing. The effect of Nurr1 on HIV silencing is direct: Nurr1 binds directly to the specific consensus binding sites in the U3 region of the HIV LTR and mutation of the Nurr1 DNA binding domain blocked its ability to suppress HIV-1 transcription. Chromatin immunoprecipitation (ChIP) assays also showed that after Nurr1 binding to the LTR, the CoREST/HDAC1/G9a/EZH2 transcription repressor complex is recruited to the HIV provirus. Finally, transcriptomic studies demonstrated that in addition to repressing HIV transcription, Nurr1 also downregulated numerous cellular genes involved in inflammation, cell cycle, and metabolism, further promoting HIV latency and microglial homoeostasis. Nurr1 therefore plays a pivotal role in modulating the cycles of proviral reactivation by potentiating the subsequent proviral transcriptional shutdown. These data highlight the therapeutic potential of Nurr1 agonists for inducing HIV silencing and microglial homeostasis and ultimately for the amelioration of the neuroinflammation associated with HIV-associated neurocognitive disorders (HAND).

Computational image features of immune architecture is associated with clinical benefit and survival in gynecological cancers across treatment modalities

BACKGROUND

We present a computational approach (ArcTIL) for quantitative characterization of the architecture of tumor-infiltrating lymphocytes (TILs) and their interplay with cancer cells from digitized H&E-stained histology whole slide images and evaluate its prognostic role in three different gynecological cancer (GC) types and across three different treatment types (platinum, radiation and immunotherapy).

METHODS

In this retrospective study, we included 926 patients with GC diagnosed with ovarian cancer (OC), cervical cancer, and endometrial cancer with available digitized diagnostic histology slides and survival outcome information. ArcTIL features quantifying architecture and spatial interplay between immune cells and the rest of nucleated cells (mostly comprised cancer cells) were extracted from the cell cluster graphs of nuclei within the tumor epithelial nests, surrounding stroma and invasive tumor front compartments on H&E-stained slides. A Cox proportional hazards model, incorporating ArcTIL features was fit on the OC training cohort (N=51), yielding an ArcTIL signature. A unique threshold learned from the training set stratified the patients into a low and high-risk group.

RESULTS

The seven feature ArcTIL classifier was found to significantly correlate with overall survival in chemotherapy and radiotherapy-treated validation cohorts and progression-free survival in an immunotherapy-treated validation cohort. ArcTIL features relating to increased density of TILs in the epithelium and invasive tumor front were found to be associated with better survival outcomes when compared with those patients with an increased TIL density in the stroma. A statistically significant association was found between the ArcTIL signature and signaling pathways for blood vessel morphogenesis, vasculature development, regulation of cell differentiation, cell-substrate adhesion, biological adhesion, regulation of vasculature development, and angiogenesis.

CONCLUSIONS

This study reveals that computationally-derived features from the spatial architecture of TILs and tumor cells are prognostic in GCs treated with chemotherapy, radiotherapy, and checkpoint blockade and are closely associated with central biological processes that impact tumor progression. These findings could aid in identifying therapy-refractory patients and further enable personalized treatment decision-making.

A neural network-based method for exhaustive cell label assignment using single cell RNA-seq data

The fast-advancing single cell RNA sequencing (scRNA-seq) technology enables researchers to study the transcriptome of heterogeneous tissues at a single cell level. The initial important step of analyzing scRNA-seq data is usually to accurately annotate cells. The traditional approach of annotating cell types based on unsupervised clustering and marker genes is time-consuming and laborious. Taking advantage of the numerous existing scRNA-seq databases, many supervised label assignment methods have been developed. One feature that many label assignment methods shares is to label cells with low confidence as "unassigned." These unassigned cells can be the result of assignment difficulties due to highly similar cell types or caused by the presence of unknown cell types. However, when unknown cell types are not expected, existing methods still label a considerable number of cells as unassigned, which is not desirable. In this work, we develop a neural network-based cell annotation method called NeuCA (Neural network-based Cell Annotation) for scRNA-seq data obtained from well-studied tissues. NeuCA can utilize the hierarchical structure information of the cell types to improve the annotation accuracy, which is especially helpful when data contain closely correlated cell types. We show that NeuCA can achieve more accurate cell annotation results compared with existing methods. Additionally, the applications on eight real datasets show that NeuCA has stable performance for intra- and inter-study annotation, as well as cross-condition annotation. NeuCA is freely available as an R/Bioconductor package at https://bioconductor.org/packages/NeuCA .

Inhibition of SC4MOL and HSD17B7 shifts cellular sterol composition and promotes oligodendrocyte formation

While the cholesterol biosynthesis pathway has been extensively studied, recent work has forged new links between inhibition of specific sterol pathway enzymes, accumulation of their unique sterol substrates, and biological areas as diverse as cancer, immunology, and neurodegenerative disease. We recently reported that dozens of small molecules enhance formation of oligodendrocytes, a glial cell type lost in multiple sclerosis, by inhibiting CYP51, Sterol 14-reductase, or EBP and inducing cellular accumulation of their 8,9-unsaturated sterol substrates. Several adjacent pathway enzymes also have 8,9-unsaturated sterol substrates but have not yet been evaluated as potential targets for oligodendrocyte formation or in many other biological contexts, in part due to a lack of available small-molecule probes. Here, we show that genetic suppression of SC4MOL or HSD17B7 increases the formation of oligodendrocytes. Additionally, we have identified and optimized multiple potent new series of SC4MOL and HSD17B7 inhibitors and shown that these small molecules enhance oligodendrocyte formation. SC4MOL inhibitor CW4142 induced accumulation of SC4MOL's sterol substrates in mouse brain and represents an in vivo probe of SC4MOL activity. Mechanistically, the cellular accumulation of these 8,9-unsaturated sterols represents a central driver of enhanced oligodendrocyte formation, as exogenous addition of purified SC4MOL and HSD17B7 substrates but not their 8,9-saturated analogs promotes OPC differentiation. Our work validates SC4MOL and HSD17B7 as novel targets for promoting oligodendrocyte formation, underlines a broad role for 8,9-unsaturated sterols as enhancers of oligodendrocyte formation, and establishes the first high-quality small molecules targeting SC4MOL and HSD17B7 as novel tools for probing diverse areas of biology.

Electric field control of magnon spin currents in an antiferromagnetic insulator

Pure spin currents can be generated via thermal excitations of magnons. These magnon spin currents serve as carriers of information in insulating materials, and controlling them using electrical means may enable energy efficient information processing. Here, we demonstrate electric field control of magnon spin currents in the antiferromagnetic insulator Cr₂O₃. We show that the thermally driven magnon spin currents reveal a spin-flop transition in thin-film Cr₂O₃. Crucially, this spin-flop can be turned on or off by applying an electric field across the thickness of the film. Using this tunability, we demonstrate electric field–induced switching of the polarization of magnon spin currents by varying only a gate voltage while at a fixed magnetic field. We propose a model considering an electric field–dependent spin-flop transition, arising from a change in sublattice magnetizations via a magnetoelectric coupling. These results provide a different approach toward controlling magnon spin current in antiferromagnets.

The effect of PEGylation on the efficacy and uptake of an immunostimulatory nanoparticle in the tumor immune microenvironment

The efficacy of immunotherapies is often limited by the immunosuppressive tumor microenvironment, which is populated with dysfunctional innate immune cells. To reprogram the tumor-resident innate immune cells, we developed immunostimulatory silica mesoporous nanoparticles (immuno-MSN). The cargo of immuno-MSN is a Stimulator of Interferon Gene (STING) agonist, which activates innate immune cells leading to production of interferon (IFN) β. By proficiently trafficking its cargo into immune cells, the immuno-MSN induced a 9-fold increase of IFN-β secretion compared to free agonist. While an external PEG shield has historically been used to protect nanoparticles from immune recognition, a PEGylated immunostimulatory nanoparticle needs to strike a balance between immune evasion to avoid off-site accumulation and uptake by target immune cells in tumors. Using the 4T1 mouse model of metastatic breast cancer and flow cytometry, it was determined that the degree of PEGylation significantly influenced the uptake of 'empty' MSNs by tumor-resident innate immune cells. This was not the case for the agonist-loaded immuno-MSN variants. It should be noted the surface charge of the 'empty' MSNs was positive rather than neutral for the agonist-loaded immuno-MSNs. However, even though the cellular uptake was similar at 24 h after injection for the three immuno-MSN variants, we observed a significant beneficial effect on the activation and expansion of APCs especially in lung metastasis using the lightly PEGylated immuno-MSN variant.

Nano-scale resolution of native retinal rod disk membranes reveals differences in lipid composition

Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.

An automated computational image analysis pipeline for histological grading of cardiac allograft rejection

AIM

Allograft rejection is a serious concern in heart transplant medicine. Though endomyocardial biopsy with histological grading is the diagnostic standard for rejection, poor inter-pathologist agreement creates significant clinical uncertainty. The aim of this investigation is to demonstrate that cellular rejection grades generated via computational histological analysis are on-par with those provided by expert pathologists.

METHODS AND RESULTS

The study cohort consisted of 2472 endomyocardial biopsy slides originating from three major US transplant centres. The 'Computer-Assisted Cardiac Histologic Evaluation (CACHE)-Grader' pipeline was trained using an interpretable, biologically inspired, 'hand-crafted' feature extraction approach. From a menu of 154 quantitative histological features relating the density and orientation of lymphocytes, myocytes, and stroma, a model was developed to reproduce the 4-grade clinical standard for cellular rejection diagnosis. CACHE-grader interpretations were compared with independent pathologists and the 'grade of record', testing for non-inferiority (δ = 6%). Study pathologists achieved a 60.7% agreement [95% confidence interval (CI): 55.2-66.0%] with the grade of record, and pair-wise agreement among all human graders was 61.5% (95% CI: 57.0-65.8%). The CACHE-Grader met the threshold for non-inferiority, achieving a 65.9% agreement (95% CI: 63.4-68.3%) with the grade of record and a 62.6% agreement (95% CI: 60.3-64.8%) with all human graders. The CACHE-Grader demonstrated nearly identical performance in internal and external validation sets (66.1% vs. 65.8%), resilience to inter-centre variations in tissue processing/digitization, and superior sensitivity for high-grade rejection (74.4% vs. 39.5%, P < 0.001).

CONCLUSION

These results show that the CACHE-grader pipeline, derived using intuitive morphological features, can provide expert-quality rejection grading, performing within the range of inter-grader variability seen among human pathologists.

Quality improvement education innovation: evaluation of Coursera MOOC 'Take the Lead on Healthcare Quality Improvement'

BACKGROUND

Massive open online courses have the potential to enable dissemination of essential components of quality improvement learning. Subsequent to conducting the massive open online course 'Take the Lead on Healthcare Quality Improvement', this paper is a report of the evaluation of the course's effectiveness in increasing healthcare professionals' quality improvement knowledge, attitudes, self-efficacy and systems thinking.

METHODS

Using the Kirkpatrick model for evaluation, a pretest-posttest design was employed to measure quality improvement knowledge, attitude, self-efficacy and systems thinking. Interprofessional learners across the globe enrolled in the 5-week online course that consisted of 10 modules (short theory bursts, assignments and assessments). The objective of the course was to facilitate learners' completion of a personal or clinical project. Of the 5751 learners enrolled, 1415 completed the demographic survey, and 88 completed all the surveys, assignments and assessments. This paper focuses on the 88 who completed the course.

RESULTS

There was a significant 14% increase in knowledge, a 3.5% increase in positive attitude, a 3.9% increase in systems thinking and a 21% increase in self-efficacy. Learners were very satisfied with the course (8.9/10).

CONCLUSIONS

Learners who completed the course 'Take the Lead on Healthcare Quality Improvement' had significant gains in learner outcomes: quality improvement knowledge, attitude, self-efficacy and systems thinking supporting this course format's efficacy in improving key components of students' quality improvement capabilities.

An Integrated Multi-Function Heterogeneous Biochemical Circuit for High-Resolution Electrochemistry-Based Genetic Analysis

Modular construction of an autonomous and programmable multi-functional heterogeneous biochemical circuit that can identify, transform, translate, and amplify biological signals into physicochemical signals based on logic design principles can be a powerful means for the development of a variety of biotechnologies. To explore the conceptual validity, we design a CRISPR-array-mediated primer-exchange-reaction-based biochemical circuit cascade, which probes a specific biomolecular input, transform the input into a structurally accessible form for circuit wiring, translate the input information into an arbitrary sequence, and finally amplify the prescribed sequence through autonomous formation of a signaling concatemer. This upstream biochemical circuit is further wired with a downstream electrochemical interface, delivering an integrated bioanalytical platform. We program this platform to directly analyze the genome of SARS-CoV-2 in human cell lysate, demonstrating the capability and the utility of this unique integrated system.

Water transport mediated by murine urea transporters: implications for urine concentration mechanisms

Urea transporters (UTs) facilitate urea diffusion across cell membranes and play an important role in the urinary concentration mechanisms in the kidney. Herein, we injected cRNAs encoding for c-Myc-tagged murine UT-B, UT-A2 or UT-A3 (versus water-injected control) in Lithobates oocytes and evaluated oocyte surface protein expression with biotinylation and immunoblotting, urea uptake using [14C] counts and water permeability (P f ) by video microscopy. Immunoblots of UT-injected oocyte membranes revealed bands with a molecular weight consistent with that of a UT monomer (34 kDa), and UT-injected oocytes displayed significantly increased and phloretin-sensitive urea uptake and P f when compared to day-matched control oocytes. Subtracting the water-injected urea uptake or P f values from those of UT-injected oocytes yielded UT-dependent values*. We demonstrate for the first time that UT-A2 and UT-A3 can transport water, and we confirm that UT-B is permeable to water. Moreover, the [14C] urea*/P f * ratios fell in the sequence mUT-B>mUT-A2>mUT-A3, indicating that UTs can exhibit selectivity to urea and/or water. It is likely that specific kidney regions with high levels of UTs will exhibit increased urea and/or water permeabilities, directly influencing urine concentration. Furthermore, UT-mediated water transport activity must be considered when developing UT-inhibitors as novel diuretics.This article has an associated First Person interview with the first author of the paper.

Manipulating acoustic and plasmonic modes in gold nanostars

In this contribution experimental evidence of plasmonic edge modes and acoustic breathing modes in gold nanostars (AuNSs) is reported. AuNSs are synthesized by a surfactant-free, one-step wet-chemistry method. Optical extinction measurements of AuNSs confirm the presence of localized surface plasmon resonances (LSPRs), while electron energy-loss spectroscopy (EELS) using a scanning transmission electron microscope (STEM) shows the spatial distribution of LSPRs and reveals the presence of acoustic breathing modes. Plasmonic hot-spots generated at the pinnacle of the sharp spikes, due to the optically active dipolar edge mode, allow significant intensity enhancement of local fields and hot-electron injection, and are thus useful for size detection of small protein molecules. The breathing modes observed away from the apices of the nanostars are identified as stimulated dark modes - they have an acoustic nature - and likely originate from the confinement of the surface plasmon by the geometrical boundaries of a nanostructure. The presence of both types of modes is verified by numerical simulations. Both these modes offer the possibility of designing nanoplasmonic antennas based on AuNSs, which can provide information on both mass and polarizability of biomolecules using a two-step molecular detection process.

Effect of chloride substitution on interfacial charge transfer processes in MAPbI3 perovskite thin film solar cells: planar versus mesoporous

For photovoltaic devices based on hybrid organic-inorganic perovskite thin films, the cell architecture is a vital parameter in defining the macroscopic performance. However, the understanding of the correlation between architecture and carrier dynamics in perovskite thin films has remained elusive. In this work, we utilize concerted materials characterization and optical measurements to investigate the role of chloride addition in PSC devices with two different architectures. Perovskite thin films, prepared with varying ratios of methylammonium halide MACl : MAI (0 : 1, 0.5 : 1, 1 : 1, and 2 : 1), were coated on either planar or mesoporous TiO₂/FTO substrates. X-ray diffraction analysis reveals that with increasing the ratio of the Cl^- precursor, there is an increasing preferential directional growth of the perovskite film in both configurations. Time-resolved photoluminescence spectroscopy was applied to investigate the electron injection dynamics from the photoexcited perovskites to the TiO₂. It is found that the interfacial electron injection rate from perovskite to planar TiO₂ is accelerated with increasing Cl^- content, which explains the increased power conversion efficiencies using Cl^--modified perovskites as photoactive materials. In contrast, Cl^- addition demonstrate no discernable influence on electron injection to mesoporous TiO₂, suggesting the interfacial charge recombination rather than electron injection give rise to the improved performance observed in the mesoporous configuration. The results presented here, provide a deeper understanding of the mechanism of chloride addition to MAPbI₃ solar cells with different architectures.

Radiocarbon chronology of Manot Cave, Israel and Upper Paleolithic dispersals

The timing of archeological industries in the Levant is central for understanding the spread of modern humans with Upper Paleolithic traditions. We report a high-resolution radiocarbon chronology for Early Upper Paleolithic industries (Early Ahmarian and Levantine Aurignacian) from the newly excavated site of Manot Cave, Israel. The dates confirm that the Early Ahmarian industry was present by 46,000 calibrated years before the present (cal BP), and the Levantine Aurignacian occurred at least between 38,000 and 34,000 cal BP. This timing is consistent with proposed migrations or technological diffusions between the Near East and Europe. Specifically, the Ahmarian could have led to the development of the Protoaurignacian in Europe, and the Aurignacian in Europe could have spread back to the Near East as the Levantine Aurignacian.