Validation of mitotic cell quantification via microscopy and multiple whole-slide scanners

BACKGROUND

The establishment of whole-slide imaging (WSI) as a medical diagnostic device allows that pathologists may evaluate mitotic activity with this new technology. Furthermore, the image digitalization provides an opportunity to develop algorithms for automatic quantifications, ideally leading to improved reproducibility as compared to the naked eye examination by pathologists. In order to implement them effectively, accuracy of mitotic figure detection using WSI should be investigated. In this study, we aimed to measure pathologist performance in detecting mitotic figures (MFs) using multiple platforms (multiple scanners) and compare the results with those obtained using a brightfield microscope.

METHODS

Four slides of canine oral melanoma were prepared and digitized using 4 WSI scanners. In these slides, 40 regions of interest (ROIs) were demarcated, and five observers identified the MFs using different viewing modes: microscopy and WSI. We evaluated the inter- and intra-observer agreements between modes with Cohen's Kappa and determined "true" MFs with a consensus panel. We then assessed the accuracy (agreement with truth) using the average of sensitivity and specificity.

RESULTS

In the 40 ROIs, 155 candidate MFs were detected by five pathologists; 74 of them were determined to be true MFs. Inter- and intra-observer agreement was mostly "substantial" or greater (Kappa = 0.594-0.939). Accuracy was between 0.632 and 0.843 across all readers and modes. After averaging over readers for each modality, we found that mitosis detection accuracy for 3 of the 4 WSI scanners was significantly less than that of the microscope (p = 0.002, 0.012, and 0.001).

CONCLUSIONS

This study is the first to compare WSIs and microscopy in detecting MFs at the level of individual cells. Our results suggest that WSI can be used for mitotic cell detection and offers similar reproducibility to the microscope, with slightly less accuracy.

Loss of IRF2BPL impairs neuronal maintenance through excess Wnt signaling

De novo truncations in Interferon Regulatory Factor 2 Binding Protein Like (IRF2BPL) lead to severe childhood-onset neurodegenerative disorders. To determine how loss of IRF2BPL causes neural dysfunction, we examined its function in Drosophila and zebrafish. Overexpression of either IRF2BPL or Pits, the Drosophila ortholog, represses Wnt transcription in flies. In contrast, neuronal depletion of Pits leads to increased wingless (wg) levels in the brain and is associated with axonal loss, whereas inhibition of Wg signaling is neuroprotective. Moreover, increased neuronal expression of wg in flies is sufficient to cause age-dependent axonal loss, similar to reduction of Pits. Loss of irf2bpl in zebrafish also causes neurological defects with an associated increase in wnt1 transcription and downstream signaling. WNT1 is also increased in patient-derived astrocytes, and pharmacological inhibition of Wnt suppresses the neurological phenotypes. Last, IRF2BPL and the Wnt antagonist, CKIα, physically and genetically interact, showing that IRF2BPL and CkIα antagonize Wnt transcription and signaling.

Circadian control of heparan sulfate levels times phagocytosis of amyloid beta aggregates

Alzheimer's Disease (AD) is a neuroinflammatory disease characterized partly by the inability to clear, and subsequent build-up, of amyloid-beta (Aβ). AD has a bi-directional relationship with circadian disruption (CD) with sleep disturbances starting years before disease onset. However, the molecular mechanism underlying the relationship of CD and AD has not been elucidated. Myeloid-based phagocytosis, a key component in the metabolism of Aβ, is circadianly-regulated, presenting a potential link between CD and AD. In this work, we revealed that the phagocytosis of Aβ42 undergoes a daily circadian oscillation. We found the circadian timing of global heparan sulfate proteoglycan (HSPG) biosynthesis was the molecular timer for the clock-controlled phagocytosis of Aβ and that both HSPG binding and aggregation may play a role in this oscillation. These data highlight that circadian regulation in immune cells may play a role in the intricate relationship between the circadian clock and AD.

De novo variants in EMC1 lead to neurodevelopmental delay and cerebellar degeneration and affect glial function in Drosophila

BACKGROUND

The endoplasmic reticulum (ER)-membrane protein complex (EMC) is a multi-protein transmembrane complex composed of 10 subunits that functions as a membrane-protein chaperone. Variants in EMC1 lead to neurodevelopmental delay and cerebellar degeneration. Multiple families with biallelic variants have been published, yet to date, only a single report of a monoallelic variant has been described, and functional evidence is sparse.

METHODS

Exome sequencing was used to investigate the genetic cause underlying severe developmental delay in three unrelated children. EMC1 variants were modeled in Drosophila, using loss-of-function (LoF) and overexpression studies. Glial-specific and neuronal-specific assays were used to determine whether the dysfunction was specific to one cell type.

RESULTS

Exome sequencing identified de novo variants in EMC1 in three individuals affected by global developmental delay, hypotonia, seizures, visual impairment and cerebellar atrophy. All variants were located at Pro582 or Pro584. Drosophila studies indicated that imbalance of EMC1-either overexpression or knockdown-results in pupal lethality and suggest that the tested homologous variants are LoF alleles. In addition, glia-specific gene dosage, overexpression or knockdown, of EMC1 led to lethality, whereas neuron-specific alterations were tolerated.

DISCUSSION

We establish de novo monoallelic EMC1 variants as causative of a neurological disease trait by providing functional evidence in a Drosophila model. The identified variants failed to rescue the lethality of a null allele. Variations in dosage of the wild-type EMC1, specifically in glia, lead to pupal lethality, which we hypothesize results from the altered stoichiometry of the multi-subunit protein complex EMC.

Meta-reinforcement learning via orbitofrontal cortex

The meta-reinforcement learning (meta-RL) framework, which involves RL over multiple timescales, has been successful in training deep RL models that generalize to new environments. It has been hypothesized that the prefrontal cortex may mediate meta-RL in the brain, but the evidence is scarce. Here we show that the orbitofrontal cortex (OFC) mediates meta-RL. We trained mice and deep RL models on a probabilistic reversal learning task across sessions during which they improved their trial-by-trial RL policy through meta-learning. Ca2+/calmodulin-dependent protein kinase II-dependent synaptic plasticity in OFC was necessary for this meta-learning but not for the within-session trial-by-trial RL in experts. After meta-learning, OFC activity robustly encoded value signals, and OFC inactivation impaired the RL behaviors. Longitudinal tracking of OFC activity revealed that meta-learning gradually shapes population value coding to guide the ongoing behavioral policy. Our results indicate that two distinct RL algorithms with distinct neural mechanisms and timescales coexist in OFC to support adaptive decision-making.

Synaptic vesicle proteins are selectively delivered to axons in mammalian neurons

Neurotransmitter-filled synaptic vesicles (SVs) mediate synaptic transmission and are a hallmark specialization in neuronal axons. Yet, how SV proteins are sorted to presynaptic nerve terminals remains the subject of debate. The leading model posits that these proteins are randomly trafficked throughout neurons and are selectively retained in presynaptic boutons. Here, we used the RUSH (retention using selective hooks) system, in conjunction with HaloTag labeling approaches, to study the egress of two distinct transmembrane SV proteins, synaptotagmin 1 and synaptobrevin 2, from the soma of mature cultured rat and mouse neurons. For these studies, the SV reporter constructs were expressed at carefully controlled, very low levels. In sharp contrast to the selective retention model, both proteins selectively and specifically entered axons with minimal entry into dendrites. However, even moderate overexpression resulted in the spillover of SV proteins into dendrites, potentially explaining the origin of previous non-polarized transport models, revealing the limited, saturable nature of the direct axonal trafficking pathway. Moreover, we observed that SV constituents were first delivered to the presynaptic plasma membrane before incorporation into SVs. These experiments reveal a new-found membrane trafficking pathway, for SV proteins, in classically polarized mammalian neurons and provide a glimpse at the first steps of SV biogenesis.

Therapeutic genetic variation revealed in diverse Hsp104 homologs

The AAA+ protein disaggregase, Hsp104, increases fitness under stress by reversing stress-induced protein aggregation. Natural Hsp104 variants might exist with enhanced, selective activity against neurodegenerative disease substrates. However, natural Hsp104 variation remains largely unexplored. Here, we screened a cross-kingdom collection of Hsp104 homologs in yeast proteotoxicity models. Prokaryotic ClpG reduced TDP-43, FUS, and α-synuclein toxicity, whereas prokaryotic ClpB and hyperactive variants were ineffective. We uncovered therapeutic genetic variation among eukaryotic Hsp104 homologs that specifically antagonized TDP-43 condensation and toxicity in yeast and TDP-43 aggregation in human cells. We also uncovered distinct eukaryotic Hsp104 homologs that selectively antagonized α-synuclein condensation and toxicity in yeast and dopaminergic neurodegeneration in C. elegans. Surprisingly, this therapeutic variation did not manifest as enhanced disaggregase activity, but rather as increased passive inhibition of aggregation of specific substrates. By exploring natural tuning of this passive Hsp104 activity, we elucidated enhanced, substrate-specific agents that counter proteotoxicity underlying neurodegeneration.

Dynamic and selective engrams emerge with memory consolidation

Episodic memories are encoded by experience-activated neuronal ensembles that remain necessary and sufficient for recall. However, the temporal evolution of memory engrams after initial encoding is unclear. In this study, we employed computational and experimental approaches to examine how the neural composition and selectivity of engrams change with memory consolidation. Our spiking neural network model yielded testable predictions: memories transition from unselective to selective as neurons drop out of and drop into engrams; inhibitory activity during recall is essential for memory selectivity; and inhibitory synaptic plasticity during memory consolidation is critical for engrams to become selective. Using activity-dependent labeling, longitudinal calcium imaging and a combination of optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted contextual fear conditioning experiments that supported our model's predictions. Our results reveal that memory engrams are dynamic and that changes in engram composition mediated by inhibitory plasticity are crucial for the emergence of memory selectivity.

The fly homolog of SUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival

SUPT16H encodes the large subunit of the FAcilitate Chromatin Transcription (FACT) complex, which functions as a nucleosome organizer during transcription. We identified two individuals from unrelated families carrying de novo missense variants in SUPT16H. The probands exhibit global developmental delay, intellectual disability, epilepsy, facial dysmorphism and brain structural abnormalities. We used Drosophila to characterize two variants: p.T171I and p.G808R. Loss of the fly ortholog, dre4, causes lethality at an early developmental stage. RNAi-mediated knockdown of dre4 in either glia or neurons causes severely reduced eclosion and longevity. Tissue-specific knockdown of dre4 in the eye or wing leads to the loss of these tissues, whereas overexpression of SUPT16H has no dominant effect. Moreover, expression of the reference SUPT16H significantly rescues the loss-of-function phenotypes in the nervous system as well as wing and eye. In contrast, expression of SUPT16H p.T171I or p.G808R rescues the phenotypes poorly, indicating that the variants are partial loss-of-function alleles. While previous studies argued that the developmental arrest caused by loss of dre4 is due to impaired ecdysone production in the prothoracic gland, our data show that dre4 is required for proper cell growth and survival in multiple tissues in a cell-autonomous manner. Altogether, our data indicate that the de novo loss-of-function variants in SUPT16H are indeed associated with developmental and neurological defects observed in the probands.

The Costly Vicious Cycle of Infections and Malnutrition

Malnutrition, which continues to affect hundreds of millions of people worldwide, is both a cause and consequence of a range of infectious diseases. In this perspective piece, we provide an overview of the bidirectional relationship between malnutrition and infectious diseases. In addition to enteric infections, we use tuberculosis as a case study of this relationship between malnutrition and infectious diseases, and to demonstrate the potential of nutritional interventions to mitigate mortality and morbidity from infectious diseases. We conclude with suggestions on advancing our understanding of the vicious cycle of microbes and malnutrition and finding ways to break it.

Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology

RNA undergoes complex posttranscriptional processing including chemical modifications of the nucleotides. The resultant-modified nucleotides are an integral part of RNA sequences that must be considered in studying the biology of RNA and in the design of RNA therapeutics. However, the current "RNA-sequencing" methods primarily sequence complementary DNA rather than RNA itself, which means that the modifications present in RNA are not captured in the sequencing results. Emerging direct RNA-sequencing technologies, such as those offered by Oxford Nanopore, aim to address this limitation. In this study, we synthesized and used Nanopore technology to sequence RNA transcripts consisting of canonical nucleotides and 10 different modifications in various concentrations. The results show that direct RNA sequencing still has a baseline error rate of >10%, and although some modifications can be detected, many remain unidentified. Thus, there is a need to develop sequencing technologies and analysis methods that can comprehensively capture the total complexity of RNA. The RNA sequences obtained through this project are made available for benchmarking analysis methods.

Nutritionally acquired immunodeficiency must be addressed with the same urgency as HIV to end tuberculosis

Tuberculosis (TB) is the leading infectious killer worldwide, with 10.6 million cases and 1.6 million deaths in 2021 alone. One in 5 incident TB cases were attributable to malnutrition, more than double the fraction attributed to HIV. Like HIV, malnutrition is a cause of secondary immunodeficiency and has even been dubbed nutritionally acquired immunodeficiency syndrome (N-AIDS). However, malnutrition remains the neglected cousin of HIV in global TB elimination efforts. Malnutrition increases the risk for TB progression, increases disease severity, and worsens TB treatment outcomes. Thus, it is both a TB determinant and comorbidity. In this perspective, we discuss decades of data to make the case that N-AIDS, just like HIV/AIDS, also deserves special consideration in the TB elimination discourse. Fortunately, malnutrition is a modifiable risk factor and there is now empirical evidence that addressing nutrition can help us curb the TB pandemic. Recognizing malnutrition as a key determinant and comorbidity is key to detecting and treating the missing millions while also preventing additional millions from suffering TB disease.

Paid summer undergraduate internships are one strategy to increase diversity in genetic counseling

The genetic counseling profession has attempted to enhance the diversity of its workforce since its inception but does not yet reflect the demographics of the United States. One barrier to entry into genetic counseling programs may be the ability to gain exposure to the profession prior to applying for entry. Many applicants participate in unpaid shadowing experiences, which could be a limitation to students from underrepresented backgrounds who may be less familiar with the field or who cannot forgo a salary. To address this concern, the University of Pennsylvania Master of Science in Genetic Counseling Program developed a six-week, paid summer internship designed for undergraduates interested in genetic counseling and from underrepresented backgrounds in the field. Students were recruited via social media and word of mouth. Three undergraduates participated in the first year and four in the second year. Participants received lectures on basic topics in genetics and medical genetics, engaged in workshops and panel discussions, attended rounds and case conferences, interacted with genetic counseling mentors, and were able to shadow genetic counselors in the clinic. Benefits to the interns included enhanced appreciation for the field, development of connections with practicing genetic counselors, and development of connections with each other. The program received positive and constructive feedback and has been continued for future summers.

Spillover effect of the Patient Drive Payment Model on skilled nursing facility therapy delivery among Medicare Advantage enrollees

In a multi-payer health care system, economic theory suggests that different payers can impose spillover effects on one another. This study aimed to evaluate the spillover effect of the Patient Driven Payment Model (PDPM) on Medicare Advantage (MA) enrollees, despite it being designed for Traditional Medicare (TM) beneficiaries. We applied a regression discontinuity approach by comparing therapy utilization before and after the implementation of PDPM in October 2019 focusing on patients newly admitted to skilled nursing facilities. The results showed that both TM and MA enrollees experienced a decrease in individual therapy minutes and an increase in non-individual therapy minutes. The estimated reduction in total therapy use was 9 min per day for TM enrollees and 3 min per day for MA enrollees. The effect of PDPM on MA beneficiaries varied depending on the level of MA penetration, with the smallest effect in facilities with the highest MA penetration quartile. In summary, the PDPM had directionally similar effects on therapy utilization for both TM and MA enrollees, but the magnitudes were smaller for MA beneficiaries. These results suggest that policy changes intended for TM beneficiaries may spillover to MA enrollees and should be assessed accordingly.

Retinal mid-peripheral capillary free zones are enlarged in cognitively unimpaired older adults at high risk for Alzheimer's disease

BACKGROUND

Compared to standard neuro-diagnostic techniques, retinal biomarkers provide a probable low-cost and non-invasive alternative for early Alzheimer's disease (AD) risk screening. We have previously quantified the periarteriole and perivenule capillary free zones (mid-peripheral CFZs) in cognitively unimpaired (CU) young and older adults as novel metrics of retinal tissue oxygenation. There is a breakdown of the inner retinal blood barrier, pericyte loss, and capillary non-perfusion or dropout in AD leading to potential enlargement of the mid-peripheral CFZs. We hypothesized the mid-peripheral CFZs will be enlarged in CU older adults at high risk for AD compared to low-risk individuals.

METHODS

20 × 20° optical coherence tomography angiography images consisting of 512 b-scans, 512 A-scans per b-scan, 12-µm spacing between b-scans, and 5 frames averaged per each b-scan location of the central fovea and of paired major arterioles and venules with their surrounding capillaries inferior to the fovea of 57 eyes of 37 CU low-risk (mean age: 66 years) and 50 eyes of 38 CU high-risk older adults (mean age: 64 years; p = 0.24) were involved in this study. High-risk participants were defined as having at least one APOE e4 allele and a positive first-degree family history of AD while low-risk participants had neither of the two criteria. All participants had Montreal Cognitive Assessment scores ≥ 26. The mid-peripheral CFZs were computed in MATLAB and compared between the two groups.

RESULTS

The periarteriole CFZ of the high-risk group (75.8 ± 9.19 µm) was significantly larger than that of the low-risk group (71.3 ± 7.07 µm), p = 0.005, Cohen's d = 0.55. The perivenule CFZ of the high-risk group (60.4 ± 8.55 µm) was also significantly larger than that of the low-risk group (57.3 ± 6.40 µm), p = 0.034, Cohen's d = 0.42. There were no significant differences in foveal avascular zone (FAZ) size, FAZ effective diameter, and vessel density between the two groups, all p > 0.05.

CONCLUSIONS

Our results show larger mid-peripheral CFZs in CU older adults at high risk for AD, with the potential for the periarteriole CFZ to serve as a novel retinal vascular biomarker for early AD risk detection.

Secure and scalable gene expression quantification with pQuant

Next generation sequencing reads from RNA-seq studies expose private genotypes of individuals during computation. Here, we introduce pQuant, an algorithm that employs homomorphic encryption to ensure privacy-preserving quantification of gene expression from RNA-seq data across public and cloud servers. pQuant performs computations on encrypted data, allowing researchers to handle sensitive information without exposing it. Our evaluations demonstrate that pQuant achieves accuracy comparable to state-of-the-art non-secure algorithms like STAR and kallisto. pQuant is highly scalable and its runtime and memory do not depend on the number of reads. It also supports parallel processing to enhance efficiency regardless of the number of genes analyzed.

Association and multimodal model of retinal and blood-based biomarkers for detection of preclinical Alzheimer's disease

BACKGROUND

The potential diagnostic value of plasma amyloidogenic beta residue 42/40 ratio (Aβ42/Aβ40 ratio), neurofilament light (NfL), tau phosphorylated at threonine-181 (p-tau181), and threonine-217 (p-tau217) has been extensively discussed in the literature. We have also previously described the association between retinal biomarkers and preclinical Alzheimer's disease (AD). The goal of this study was to evaluate the association, and a multimodal model of, retinal and plasma biomarkers for detection of preclinical AD.

METHODS

We included 82 cognitively unimpaired (CU) participants (141 eyes; mean age: 67 years; range: 56-80) from the Atlas of Retinal Imaging in Alzheimer's Study (ARIAS). Blood samples were assessed for concentrations of Aβ42/Aβ40 ratio, NfL, p-tau181, and p-tau217 (ALZpath, Inc.) using Single molecule array (SIMOA) technology. The Spectralis II system (Heidelberg Engineering) was used to acquire macular centered Spectral Domain Optical Coherence Tomography (SD-OCT) images for evaluation of putative retinal gliosis surface area and macular retinal nerve fiber layer (mRNFL) thickness. For all participants, correlations (adjusted for age and correlation between eyes) were assessed between retinal and blood-based biomarkers. A subgroup cohort of 57 eyes from 32 participants with recent Aβ positron emission tomography (PET) results, comprising 18 preclinical patients (Aβ PET + ve, 32 eyes) and 14 controls (Aβ PET -ve, 25 eyes) with a mean age of 69 vs. 66, p = 0.06, was included for the assessment of a multimodal model to distinguish between the two groups. For this subgroup cohort, receiver operating characteristic (ROC) analysis was performed to compare the multimodal model of retinal and plasma biomarkers vs. each biomarker alone to distinguish between the two groups.

RESULTS

Significant correlation was found between putative retinal gliosis and p-tau217 in the univariate mixed model (β = 0.48, p = 0.007) but not for the other plasma biomarkers (p > 0.05). This positive correlation was also retained in the multivariate mixed model (β = 0.43, p = 0.022). The multimodal ROC model based on retinal (gliosis area, inner inferior RNFL thickness, inner superior RNFL thickness, and inner nasal RNFL thickness) and plasma biomarkers (p-tau217 and Aβ42/Aβ40 ratio) had an excellent AUC of 0.97 (95% CI = 0.93-1.01; p < 0.001) compared to unimodal models of retinal and plasma biomarkers.

CONCLUSIONS

Our analyses show the potential of integrating retinal and blood-based biomarkers for improved detection and screening of preclinical AD.

Color Standardization and Stain Intensity Calibration for Whole Slide Image-Based Immunohistochemistry Assessment

Automated quantification of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) using whole slide imaging (WSI) is expected to eliminate subjectivity in visual assessment. However, the color intensity in WSI varies depending on the staining process and scanner device. Such variations affect the image analysis results. This paper presents methods to diminish the influence of color variation produced in the staining process using a calibrator slide consisting of peptide-coated microbeads. The calibrator slide is stained along with tissue sample slides, and the 3,3'-diaminobenzidine (DAB) color intensities of the microbeads are used for calibrating the color variation of the sample slides. An off-the-shelf image analysis tool is employed for the automated assessment, in which cells are classified by the thresholds for the membrane staining. We have adopted two methods for calibrating the color variation based on the DAB color intensities obtained from the calibrator slide: (1) thresholds for classifying the DAB membranous intensity are adjusted, and (2) the color intensity of WSI is corrected. In the experiment, the calibrator slides and tissue of breast cancer slides were stained together on different days and used to test our protocol. With the proposed protocol, the discordance in the HER2 evaluation was reduced to one slide out of 120 slides.

COVID-19 Vaccination Among Skilled Nursing Facility Staff: Challenges and Strategies Identified by Administrators

COVID-19 vaccinations are critical for mitigating outbreaks and reducing mortality for skilled nursing facility (SNF) residents and staff, yet uptake among SNF staff varies widely and remains suboptimal. Understanding which strategies are successful for promoting staff vaccination, and examining the relationship between vaccination policies and staff retention/turnover is key for identifying best practices. We conducted repeated interviews with SNF administrators at 3-month intervals between July 2020 and December 2021 (n = 156 interviews). We found that COVID-19 vaccines were initially met with both enthusiasm and skepticism by SNF staff. Administrators reported strategies to increase staff vaccine acceptance, including incentives, one-on-one education, and less stringent personal protective equipment requirements. Federal and state vaccination mandates further promoted vaccine uptake. This combination of mandates with prioritization of the vaccine by SNFs and their leadership was successful at increasing staff vaccination acceptance, which may be critical to increase staff booster uptake from its current suboptimal levels.

All the single cells: Single-cell transcriptomics/epigenomics experimental design and analysis considerations for glial biologists

Single-cell transcriptomics, epigenomics, and other 'omics applied at single-cell resolution can significantly advance hypotheses and understanding of glial biology. Omics technologies are revealing a large and growing number of new glial cell subtypes, defined by their gene expression profile. These subtypes have significant implications for understanding glial cell function, cell-cell communications, and glia-specific changes between homeostasis and conditions such as neurological disease. For many, the training in how to analyze, interpret, and understand these large datasets has been through reading and understanding literature from other fields like biostatistics. Here, we provide a primer for glial biologists on experimental design and analysis of single-cell RNA-seq datasets. Our goal is to further the understanding of why decisions are made about datasets and to enhance biologists' ability to interpret and critique their work and the work of others. We review the steps involved in single-cell analysis with a focus on decision points and particular notes for glia. The goal of this primer is to ensure that single-cell 'omics experiments continue to advance glial biology in a rigorous and replicable way.

The ABCDs of Nutritional Assessment in Infectious Diseases Research

Malnutrition is the most common acquired cause of immunodeficiency worldwide. Nutritional deficiencies can blunt both the innate and adaptive immune response to pathogens. Furthermore, malnutrition is both a cause and consequence of infectious diseases. The bidirectional relationship between infectious diseases and undernutrition, as well as the inflammatory milieu of infectious diseases, can complicate nutritional assessment. This article aims to provide clinicians and researchers with an overview of commonly used tools to assess nutritional status, with a particular emphasis on their use in the context of infectious diseases. These tools include anthropometric, biochemical, clinical/physical, and dietary assessments to screen and evaluate undernutrition, diet quality, and food insecurity effectively.

National Institutes of Health Funding for Tuberculosis Comorbidities Is Disproportionate to Their Epidemiologic Impact

Tuberculosis (TB) is a leading infectious killer worldwide. We systematically searched the National Institutes of Health Research, Portfolio Online Reporting Tools Expenditures and Results (RePORTER) website to compare research funding for key TB comorbidities-undernutrition, alcohol use, human immunodeficiency virus, tobacco use, and diabetes-and found a large mismatch between the population attributable fraction of these risk factors and the funding allocated to them.

Trends in hospital discharge outcomes among high-risk Medicare beneficiaries before and during the COVID-19 pandemic

Introduction

Medicare beneficiaries face significant health risks and care disruptions during public health emergencies, but little is known about how care patterns evolved throughout the COVID-19 pandemic or differed between traditional Medicare (TM) and Medicare Advantage (MA).

Methods

Using Medicare claims data for over 20 million hospital discharges during 2018-2022, we examined trends in hospital length of stay, discharge disposition, and mortality among beneficiaries with 5 major comorbidities (dementia, diabetes, congestive heart failure, hip fracture, and stroke), stratified by COVID status and payer type.

Results

We found that COVID patients initially experienced substantially longer hospital stays (8.3 vs 4.6 days) and higher 30-day mortality (34% vs 5%) compared to patients without COVID. MA beneficiaries showed consistently higher home health utilization but similar mortality patterns to TM enrollees. By mid-2022, most outcome differences had converged between COVID and non-COVID patients, suggesting health system adaptation to the pandemic.

Conclusion

Our findings highlight how the pandemic was associated with shifts toward home-based post-acute care, emphasizing the need for policies supporting home-based care infrastructure and flexible care delivery models that could help health systems better adapt during future public health emergencies.

SARM1 loss protects retinal ganglion cells in a mouse model of autosomal dominant optic atrophy

Autosomal dominant optic atrophy (ADOA), the most prevalent hereditary optic neuropathy, leads to retinal ganglion cell (RGC) degeneration and vision loss. ADOA is primarily caused by mutations in the optic atrophy type 1 (OPA1) gene, which encodes a conserved GTPase important for mitochondrial inner membrane dynamics. To date, the disease mechanism remains unclear, and no therapies are available. We generated a mouse model carrying the pathogenic Opa1R290Q/+ allele that recapitulated key features of human ADOA, including mitochondrial defects, age-related RGC loss, optic nerve degeneration, and reduced RGC functions. We identified sterile alpha and TIR motif containing 1 (SARM1), a neurodegeneration switch, as a key driver of RGC degeneration in these mice. Sarm1 KO nearly completely suppressed all the degeneration phenotypes without reversing mitochondrial fragmentation. Additionally, we show that a portion of SARM1 localized within the mitochondrial intermembrane space. These findings indicated that SARM1 was activated downstream of mitochondrial dysfunction in ADOA, highlighting it as a promising therapeutic target.

Hyperoxia impairs intraflagellar transport and causes dysregulated metabolism with resultant decreased cilia length

Supplemental oxygen is a lifesaving measure in infants born premature to facilitate oxygenation. Unfortunately, it may lead to alveolar simplification and loss of proximal airway epithelial cilia. Little is known about the mechanism by which hyperoxia causes ciliary dysfunction in the proximal respiratory tract. We hypothesized that hyperoxia causes intraflagellar transport (IFT) dysfunction with resultant decreased cilia length. Differentiated basal human airway epithelial cells (HAEC) were exposed to hyperoxia or air for up to 48 h. Neonatal mice (<12 h old) were exposed to hyperoxia for 72 h and recovered in room air until postnatal day (PND) 60. Cilia length was measured from scanning electron microscopy images using a MATLAB-derived program. Proteomics and metabolomics were carried out in cells after hyperoxia. After hyperoxia, there was a significant time-dependent reduction in cilia length after hyperoxia in HAEC. Proteomic analysis showed decreased abundance of multiple proteins related to IFT including dynein motor proteins. In neonatal mice exposed to hyperoxia, there was a significant decrease in acetylated α tubulin at PND10 followed by recovery to normal levels at PND60. In HAEC, hyperoxia decreased the abundance of multiple proteins associated with complex I of the electron transport chain. In HAEC, hyperoxia increased levels of malate, fumarate, and citrate, and reduced the ATP/ADP ratio at 24 h with a subsequent increase at 36 h. Exposure to hyperoxia reduced cilia length, and this was associated with aberrant IFT protein expression and dysregulated metabolism. This suggests that hyperoxic exposure leads to aberrant IFT protein expression in the respiratory epithelium resulting in shortened cilia.