Influenza vaccine effectiveness against hospitalized SARS-CoV-2 infection.

Background: Some studies conducted before the Delta and Omicron variant-dominant periods have indicated that influenza vaccination provided protection against COVID-19 infection or hospitalization, but these results were limited by small study cohorts and a lack of comprehensive data on patient characteristics. No studies have examined this question during the Delta and Omicron periods (08/01/2021 to 2/22/2022). Methods: We conducted a retrospective cohort study of influenza-vaccinated and unvaccinated patients in the Corewell Health East(CHE, formerly known as Beaumont Health), Corewell Health West(CHW, formerly known as Spectrum Health) and Michigan Medicine (MM) healthcare system during the Delta-dominant and Omicron-dominant periods. We used a test-negative, case-control analysis to assess the effectiveness of the influenza vaccine against hospitalized SARS-CoV-2 outcome in adults, while controlling for individual characteristics as well as pandameic severity and waning immunity of COVID-19 vaccine. Results: The influenza vaccination has shown to provided some protection against SARS-CoV-2 hospitalized outcome across three main healthcare systems. CHE site (odds ratio [OR]=0.73, vaccine effectiveness [VE]=27%, 95% confidence interval [CI]: [18-35], p<0.001), CHW site (OR=0.85, VE=15%, 95% CI: [6-24], p<0.001), MM (OR=0.50, VE=50%, 95% CI: [40-58], p <0.001) and overall (OR=0.75, VE=25%, 95% CI: [20-30], p <0.001). Conclusion: The influenza vaccine provides a small degree of protection against SARS-CoV-2 infection across our study sites.

Coronavirus Disease 2019 (COVID-19) Seropositivity and Asymptomatic Rates in Healthcare Workers Are Associated with Job Function and Masking.

BACKGROUND: Although the risk of exposure to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is higher for frontline healthcare workers, not all personnel have similar risks. Determining infection rate is difficult due to the limits on testing and the high rate of asymptomatic individuals. Detection of antibodies against SARS-CoV-2 may be useful for determining prior exposure to the virus and assessing mitigation strategies, such as isolation, masks, and other protective equipment. METHODS: An online assessment that included demographic, clinical, and exposure information and a blood sample was collected from 20 614 participants out of ~43 000 total employees at Beaumont Health, which includes 8 hospitals distributed across the Detroit metropolitan area in southeast Michigan. The presence of anti-SARS-CoV-2 IgG was determined using the EUROIMMUN assay. RESULTS: A total of 1818 (8.8%) participants were seropositive between April 13 and May 28, 2020. Among the seropositive individuals, 44% reported that they were asymptomatic during the month prior to blood collection. Healthcare roles such as phlebotomy, respiratory therapy, and nursing/nursing support exhibited significantly higher seropositivity. Among participants reporting direct exposure to a Coronavirus Disease 2019 (COVID-19) positive individual, those wearing an N95/PAPR mask had a significantly lower seropositivity rate (10.2%) compared to surgical/other masks (13.1%) or no mask (17.5%). CONCLUSIONS: Direct contact with COVID-19 patients increased the likelihood of seropositivity among employees but study participants who wore a mask during COVID-19 exposures were less likely to be seropositive. Additionally, a large proportion of seropositive employees self-reported as asymptomatic. (Funded by Beaumont Health and by major donors through the Beaumont Health Foundation). CLINICALTRIALS.GOV NUMBER: NCT04349202.

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets.

BACKGROUND: Identification of transcription factors (TFs) responsible for modulation of differentially expressed genes is a key step in deducing gene regulatory pathways. Most current methods identify TFs by searching for presence of DNA binding motifs in the promoter regions of co-regulated genes. However, this strategy may not always be useful as presence of a motif does not necessarily imply a regulatory role. Conversely, motif presence may not be required for a TF to regulate a set of genes. Therefore, it is imperative to include functional (biochemical and molecular) associations, such as those found in the biomedical literature, into algorithms for identification of putative regulatory TFs that might be explicitly or implicitly linked to the genes under investigation. RESULTS: In this study, we present a Latent Semantic Indexing (LSI) based text mining approach for identification and ranking of putative regulatory TFs from microarray derived differentially expressed genes (DEGs). Two LSI models were built using different term weighting schemes to devise pair-wise similarities between 21,027 mouse genes annotated in the Entrez Gene repository. Amongst these genes, 433 were designated TFs in the TRANSFAC database. The LSI derived TF-to-gene similarities were used to calculate TF literature enrichment p-values and rank the TFs for a given set of genes. We evaluated our approach using five different publicly available microarray datasets focusing on TFs Rel, Stat6, Ddit3, Stat5 and Nfic. In addition, for each of the datasets, we constructed gold standard TFs known to be functionally relevant to the study in question. Receiver Operating Characteristics (ROC) curves showed that the log-entropy LSI model outperformed the tf-normal LSI model and a benchmark co-occurrence based method for four out of five datasets, as well as motif searching approaches, in identifying putative TFs. CONCLUSIONS: Our results suggest that our LSI based text mining approach can complement existing approaches used in systems biology research to decipher gene regulatory networks by providing putative lists of ranked TFs that might be explicitly or implicitly associated with sets of DEGs derived from microarray experiments. In addition, unlike motif searching approaches, LSI based approaches can reveal TFs that may indirectly regulate genes.

Functional cohesion of gene sets determined by latent semantic indexing of PubMed abstracts.

UNLABELLED: High-throughput genomic technologies enable researchers to identify genes that are co-regulated with respect to specific experimental conditions. Numerous statistical approaches have been developed to identify differentially expressed genes. Because each approach can produce distinct gene sets, it is difficult for biologists to determine which statistical approach yields biologically relevant gene sets and is appropriate for their study. To address this issue, we implemented Latent Semantic Indexing (LSI) to determine the functional coherence of gene sets. An LSI model was built using over 1 million Medline abstracts for over 20,000 mouse and human genes annotated in Entrez Gene. The gene-to-gene LSI-derived similarities were used to calculate a literature cohesion p-value (LPv) for a given gene set using a Fisher's exact test. We tested this method against genes in more than 6,000 functional pathways annotated in Gene Ontology (GO) and found that approximately 75% of gene sets in GO biological process category and 90% of the gene sets in GO molecular function and cellular component categories were functionally cohesive (LPv<0.05). These results indicate that the LPv methodology is both robust and accurate. Application of this method to previously published microarray datasets demonstrated that LPv can be helpful in selecting the appropriate feature extraction methods. To enable real-time calculation of LPv for mouse or human gene sets, we developed a web tool called Gene-set Cohesion Analysis Tool (GCAT). GCAT can complement other gene set enrichment approaches by determining the overall functional cohesion of data sets, taking into account both explicit and implicit gene interactions reported in the biomedical literature. AVAILABILITY: GCAT is freely available at http://binf1.memphis.edu/gcat.

Prolonged intake of coenzyme Q10 impairs cognitive functions in mice.

Coenzyme Q(10) (CoQ(10)) is widely consumed as a dietary supplement to enhance bioenergetic capacity and to ameliorate the debilitative effects of the aging process or certain pathological conditions. Our main purpose in this study was to determine whether CoQ(10) intake does indeed attenuate the age-associated losses in motor, sensory, and cognitive functions or decrease the rate of mortality in mice. Mice were fed a control nonpurified diet or that diet containing 0.68 mg/g (low dosage) or 2.6 mg/g (high dosage) CoQ(10), starting at 4 mo of age, and were tested for sensory, motor, and cognitive function at 7, 15, and 25 mo of age. Amounts of the ubiquinols CoQ(9)H(2) and CoQ(10)H(2) measured in a parallel study were augmented in the cerebral cortex but not in any other region of the brain. Intake of the low-CoQ(10) diet did not affect age-associated decrements in muscle strength, balance, coordinated running, or learning/memory, whereas intake at the higher amount increased spontaneous activity, worsened the age-related losses in acuity to auditory and shock stimuli, and impaired the spatial learning/memory of old mice. The CoQ(10) diets did not affect survivorship of mice through 25 mo of age. Our results suggest that prolonged intake of CoQ(10) in low amounts has no discernable impact on cognitive and motor functions whereas intake at higher amounts exacerbates cognitive and sensory impairments encountered in old mice. These findings do not support the notion that CoQ(10) is a fitness-enhancing or an "antiaging" substance under normal physiological conditions.

Bioinformatic analysis reveals cRel as a regulator of a subset of interferon-stimulated genes.

Interferons (IFNs) are critical to the host innate immune response by inducing the expression of a family of early response genes, denoted as IFN-stimulated genes (ISGs). The role of tyrosine phosphorylation of STAT proteins in the transcription activation of ISGs is well-documented. Recent studies have indicated that other transcription factors (TFs) are likely to play a role in regulating ISG expression. Here, we describe a novel integrative approach that combines gene expression profiling, promoter sequence analysis, and literature mining to screen candidate regulatory factors in the IFN signal transduction pathway. Application of this method identified the nuclear factor kappaB (NFkappaB) protein, cRel, as a candidate regulatory factor for a subset of ISGs in mouse embryo fibroblasts. Chromatin immunoprecipitation (ChIP) and real-time PCR assays confirmed that cRel directly binds to the promoters of several ISGs, including Cxcl10, Isg15, Gbp2, Ifit3, and Ifi203, and regulates their expression. Thus, our studies identify cRel as an important TF for ISGs, and validate the approach of using Latent Semantic Indexing (LSI)-based methods to identify regulatory factors from microarray data.

Gene tree labeling using nonnegative matrix factorization on biomedical literature.

Identifying functional groups of genes is a challenging problem for biological applications. Text mining approaches can be used to build hierarchical clusters or trees from the information in the biological literature. In particular, the nonnegative matrix factorization (NMF) is examined as one approach to label hierarchical trees. A generic labeling algorithm as well as an evaluation technique is proposed, and the effects of different NMF parameters with regard to convergence and labeling accuracy are discussed. The primary goals of this study are to provide a qualitative assessment of the NMF and its various parameters and initialization, to provide an automated way to classify biomedical data, and to provide a method for evaluating labeled data assuming a static input tree. As a byproduct, a method for generating gold standard trees is proposed.

Effect of coenzyme Q10 intake on endogenous coenzyme Q content, mitochondrial electron transport chain, antioxidative defenses, and life span of mice.

The main purpose of this study was to determine whether intake of coenzyme Q10, which can potentially act as both an antioxidant and a prooxidant, has an impact on indicators of oxidative stress and the aging process. Mice were fed diets providing daily supplements of 0, 93, or 371 mg CoQ10 /kg body weight, starting at 3.5 months of age. Effects on mitochondrial superoxide generation, activities of oxidoreductases, protein oxidative damage, glutathione redox state, and life span of male mice were determined. Amounts of CoQ9 and CoQ10, measured after 3.5 or 17.5 months of intake, in homogenates and mitochondria of liver, heart, kidney, skeletal muscle, and brain increased with the dosage and duration of CoQ10 intake in all the tissues except brain. Activities of mitochondrial electron transport chain oxidoreductases, rates of mitochondrial O2-* generation, state 3 respiration, carbonyl content, glutathione redox state of tissues, and activities of superoxide dismutase, catalase, and glutathione peroxidase, determined at 19 or 25 months of age, were unaffected by CoQ10 administration. Life span studies, conducted on 50 mice in each group, showed that CoQ10 administration had no effect on mortality. Altogether, the results indicated that contrary to the historical view, supplemental intake of CoQ10 elevates the endogenous content of both CoQ9 and CoQ10, but has no discernable effect on the main antioxidant defenses or prooxidant generation in most tissues, and has no impact on the life span of mice.

Endovascular middle cerebral artery occlusion in rats as a model for studying vascular dementia.

Vascular dementia (VaD), incorporating cognitive dysfunction with vascular disease, ranks as the second leading cause of dementia in the United States, yet no effective treatment is currently available. The challenge of defining the pathological substrates of VaD is complicated by the heterogeneous nature of cerebrovascular disease and coexistence of other pathologies, including Alzheimer's disease (AD) types of lesion. The use of rodent models of ischemic stroke may help to elucidate the type of lesions that are responsible for cognitive impairment in humans. Endovascular middle cerebral artery (MCA) occlusion in rats is considered to be a convenient and reliable model of human cerebral ischemia. Both sensorimotor and cognitive dysfunction can be induced in the rat endovascular MCA occlusion model, yet sensorimotor deficits induced by endovascular MCA occlusion may improve with time, whereas data presented in this review suggest that in rats this model can result in a progressive course of cognitive impairment that is consistent with the clinical progression of VaD. Thus far, experimental studies using this model have demonstrated a direct interaction of cerebral ischemic damage and AD-type neuropathologies in the primary ischemic area. Further, coincident to the progressive decline of cognitive function, a delayed neurodegeneration in a remote area, distal to the primary ischemic area, the hippocampus, has been demonstrated in a rat endovascular MCA occlusion model. We argue that this model could be employed to study VaD and provide insight into some of the pathophysiological mechanisms of VaD.

Gene clustering by latent semantic indexing of MEDLINE abstracts.

MOTIVATION: A major challenge in the interpretation of high-throughput genomic data is understanding the functional associations between genes. Previously, several approaches have been described to extract gene relationships from various biological databases using term-matching methods. However, more flexible automated methods are needed to identify functional relationships (both explicit and implicit) between genes from the biomedical literature. In this study, we explored the utility of Latent Semantic Indexing (LSI), a vector space model for information retrieval, to automatically identify conceptual gene relationships from titles and abstracts in MEDLINE citations. RESULTS: We found that LSI identified gene-to-gene and keyword-to-gene relationships with high average precision. In addition, LSI identified implicit gene relationships based on word usage patterns in the gene abstract documents. Finally, we demonstrate here that pairwise distances derived from the vector angles of gene abstract documents can be effectively used to functionally group genes by hierarchical clustering. Our results provide proof-of-principle that LSI is a robust automated method to elucidate both known (explicit) and unknown (implicit) gene relationships from the biomedical literature. These features make LSI particularly useful for the analysis of novel associations discovered in genomic experiments. AVAILABILITY: The 50-gene document collection used in this study can be interactively queried at http://shad.cs.utk.edu/sgo/sgo.html.

Short-term vitamin E intake fails to improve cognitive or psychomotor performance of aged mice.

The purpose of this study was to determine if relatively short-term vitamin E supplementation could reverse age-associated impairments in cognitive or motor function and the accumulated oxidative damage in the brain of aged mice. Separate groups of 5- or 20-month-old C57BL6 mice were placed on either a control diet or the same diet supplemented with alpha-tocopheryl acetate (1.65 g/kg). After 4 weeks on the diets, mice were tested for cognitive and motor functions over the next 8 weeks, during which the supplementation was maintained. Vitamin E supplementation increased the concentration of alpha-tocopherol in the cerebral cortex of both the young and old mice, but did not significantly affect oxidative damage to proteins and lipids in the brain cortex. When compared with young controls, the old control mice showed slower learning of a swim maze, longer reaction times, diminished auditory and shock-startle responsiveness, and diminished motor performance on tests of coordinated running and bridge walking. The vitamin E-administered old mice failed to show improvement of function relative to age-matched controls on any of the tests, but did show altered retention performance on the swim maze task and impaired performance in the test of coordinated running. The latter effects were not evident in young mice on the supplemented diet. Results of this study suggest that, when implemented in relatively old mice, supplementation of vitamin E is ineffective in reversing preexisting age-related impairments of cognitive or motor function, and has little effect on common measures of protein or lipid oxidative damage in the mouse brain. Moreover, the current findings indicate that vitamin E could have detrimental effects on some brain functions when implemented in older animals.