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1.
Nature ; 630(8018): 836-840, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38768634

ABSTRACT

Interactions between exoplanetary atmospheres and internal properties have long been proposed to be drivers of the inflation mechanisms of gaseous planets and apparent atmospheric chemical disequilibrium conditions1. However, transmission spectra of exoplanets have been limited in their ability to observationally confirm these theories owing to the limited wavelength coverage of the Hubble Space Telescope (HST) and inferences of single molecules, mostly H2O (ref. 2). In this work, we present the panchromatic transmission spectrum of the approximately 750 K, low-density, Neptune-sized exoplanet WASP-107b using a combination of HST Wide Field Camera 3 (WFC3) and JWST Near-Infrared Camera (NIRCam) and Mid-Infrared Instrument (MIRI). From this spectrum, we detect spectroscopic features resulting from H2O (21σ), CH4 (5σ), CO (7σ), CO2 (29σ), SO2 (9σ) and NH3 (6σ). The presence of these molecules enables constraints on the atmospheric metal enrichment (M/H is 10-18× solar3), vertical mixing strength (log10Kzz = 8.4-9.0 cm2 s-1) and internal temperature (>345 K). The high internal temperature is suggestive of tidally driven inflation4 acting on a Neptune-like internal structure, which can naturally explain the large radius and low density of the planet. These findings suggest that eccentricity-driven tidal heating is a critical process governing atmospheric chemistry and interior-structure inferences for most of the cool (<1,000 K) super-Earth-to-Saturn-mass exoplanet population.

2.
Nature ; 620(7972): 67-71, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37164036

ABSTRACT

There are no planets intermediate in size between Earth and Neptune in our Solar System, yet these objects are found around a substantial fraction of other stars1. Population statistics show that close-in planets in this size range bifurcate into two classes on the basis of their radii2,3. It is proposed that the group with larger radii (referred to as 'sub-Neptunes') is distinguished by having hydrogen-dominated atmospheres that are a few percent of the total mass of the planets4. GJ 1214b is an archetype sub-Neptune that has been observed extensively using transmission spectroscopy to test this hypothesis5-14. However, the measured spectra are featureless, and thus inconclusive, due to the presence of high-altitude aerosols in the planet's atmosphere. Here we report a spectroscopic thermal phase curve of GJ 1214b obtained with the James Webb Space Telescope (JWST) in the mid-infrared. The dayside and nightside spectra (average brightness temperatures of 553 ± 9 and 437 ± 19 K, respectively) each show more than 3σ evidence of absorption features, with H2O as the most likely cause in both. The measured global thermal emission implies that GJ 1214b's Bond albedo is 0.51 ± 0.06. Comparison between the spectroscopic phase curve data and three-dimensional models of GJ 1214b reveal a planet with a high metallicity atmosphere blanketed by a thick and highly reflective layer of clouds or haze.

3.
Am J Hum Genet ; 111(4): 626-635, 2024 04 04.
Article in English | MEDLINE | ID: mdl-38579668

ABSTRACT

Despite the importance of gene-environment interactions (GxEs) in improving and operationalizing genetic discovery, interpretation of any GxEs that are discovered can be surprisingly difficult. There are many potential biological and statistical explanations for a statistically significant finding and, likewise, it is not always clear what can be claimed based on a null result. A better understanding of the possible underlying mechanisms leading to a detected GxE can help investigators decide which are and which are not relevant to their hypothesis. Here, we provide a detailed explanation of five "phenomena," or data-generating mechanisms, that can lead to nonzero interaction estimates, as well as a discussion of specific instances in which they might be relevant. We hope that, given this framework, investigators can design more targeted experiments and provide cleaner interpretations of the associated results.


Subject(s)
Gene-Environment Interaction , Humans
4.
PLoS Genet ; 20(7): e1011288, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38990837

ABSTRACT

We examined the associations of vegetarianism with metabolic biomarkers using traditional and genetic epidemiology. First, we addressed inconsistencies in self-reported vegetarianism among UK Biobank participants by utilizing data from two dietary surveys to find a cohort of strict European vegetarians (N = 2,312). Vegetarians were matched 1:4 with nonvegetarians for non-genetic association analyses, revealing significant effects of vegetarianism in 15 of 30 biomarkers. Cholesterol measures plus vitamin D were significantly lower in vegetarians, while triglycerides were higher. A genome-wide association study revealed no genome-wide significant (GWS; 5×10-8) associations with vegetarian behavior. We performed genome-wide gene-vegetarianism interaction analyses for the biomarkers, and detected a GWS interaction impacting calcium at rs72952628 (P = 4.47×10-8). rs72952628 is in MMAA, a B12 metabolic pathway gene; B12 has major deficiency potential in vegetarians. Gene-based interaction tests revealed two significant genes, RNF168 in testosterone (P = 1.45×10-6) and DOCK4 in estimated glomerular filtration rate (eGFR) (P = 6.76×10-7), which have previously been associated with testicular and renal traits, respectively. These nutrigenetic findings indicate genotype can modify the associations between vegetarianism and health outcomes.


Subject(s)
Biomarkers , Calcium , Diet, Vegetarian , Genome-Wide Association Study , Glomerular Filtration Rate , Testosterone , Humans , Male , Glomerular Filtration Rate/genetics , Testosterone/blood , Female , Biomarkers/blood , Middle Aged , Calcium/metabolism , Polymorphism, Single Nucleotide , Vegetarians , Aged , Vitamin D/blood , Adult , Ubiquitin-Protein Ligases/genetics
5.
J Cell Sci ; 137(5)2024 03 01.
Article in English | MEDLINE | ID: mdl-38465513

ABSTRACT

Drosophila neural stem cells, or neuroblasts, rapidly proliferate during embryonic and larval development to populate the central nervous system. Neuroblasts divide asymmetrically to create cellular diversity, with each division producing one sibling cell that retains the neuroblast fate and another that differentiates into glia or neurons. This asymmetric outcome is mediated by the transient polarization of numerous factors to the cell cortex during mitosis. The powerful genetics and outstanding imaging tractability of the neuroblast make it an excellent model system for studying the mechanisms of cell polarity. This Cell Science at a Glance article and the accompanying poster explore the phases of the neuroblast polarity cycle and the regulatory circuits that control them. We discuss the key features of the cycle - the targeted recruitment of proteins to specific regions of the plasma membrane and multiple phases of highly dynamic actomyosin-dependent cortical flows that pattern both protein distribution and membrane structure.


Subject(s)
Drosophila Proteins , Neural Stem Cells , Animals , Drosophila/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Neural Stem Cells/metabolism , Neurons/metabolism , Mitosis , Cell Cycle Proteins/metabolism , Cell Polarity/physiology
6.
Proc Natl Acad Sci U S A ; 120(7): e2209414120, 2023 02 14.
Article in English | MEDLINE | ID: mdl-36749720

ABSTRACT

While social characteristics are well-known predictors of mortality, prediction models rely almost exclusively on demographics, medical comorbidities, and function. Lacking an efficient way to summarize the prognostic impact of social factor, many studies exclude social factors altogether. Our objective was to develop and validate a summary measure of social risk and determine its ability to risk-stratify beyond traditional risk models. We examined participants in the Health and Retirement Study, a longitudinal, survey of US older adults. We developed the model from a comprehensive inventory of 183 social characteristics using least absolute shrinkage and selection operator, a penalized regression approach. Then, we assessed the predictive capacity of the model and its ability to improve on traditional prediction models. We studied 8,250 adults aged ≥65 y. Within 4 y of the baseline interview, 22% had died. Drawn from 183 possible predictors, the Social Frailty Index included age, gender, and eight social predictors: neighborhood cleanliness, perceived control over financial situation, meeting with children less than yearly, not working for pay, active with children, volunteering, feeling isolated, and being treated with less courtesy or respect. In the validation cohort, predicted and observed mortality were strongly correlated. Additionally, the Social Frailty Index meaningfully risk-stratified participants beyond the Charlson score (medical comorbidity index) and the Lee Index (comorbidity and function model). The Social Frailty Index includes age, gender, and eight social characteristics and accurately risk-stratifies older adults. The model improves upon commonly used risk prediction tools and has application in clinical, population health, and research settings.


Subject(s)
Frailty , Child , Humans , Aged , Longitudinal Studies , Retirement , Sociological Factors
7.
J Biol Chem ; 300(6): 107388, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38763333

ABSTRACT

As part of the classical renin-angiotensin system, the peptidase angiotensin-converting enzyme (ACE) makes angiotensin II which has myriad effects on systemic cardiovascular function, inflammation, and cellular proliferation. Less well known is that macrophages and neutrophils make ACE in response to immune activation which has marked effects on myeloid cell function independent of angiotensin II. Here, we discuss both classical (angiotensin) and nonclassical functions of ACE and highlight mice called ACE 10/10 in which genetic manipulation increases ACE expression by macrophages and makes these mice much more resistant to models of tumors, infection, atherosclerosis, and Alzheimer's disease. In another model called NeuACE mice, neutrophils make increased ACE and these mice are much more resistant to infection. In contrast, ACE inhibitors reduce neutrophil killing of bacteria in mice and humans. Increased expression of ACE induces a marked increase in macrophage oxidative metabolism, particularly mitochondrial oxidation of lipids, secondary to increased peroxisome proliferator-activated receptor α expression, and results in increased myeloid cell ATP. ACE present in sperm has a similar metabolic effect, and the lack of ACE activity in these cells reduces both sperm motility and fertilization capacity. These nonclassical effects of ACE are not due to the actions of angiotensin II but to an unknown molecule, probably a peptide, that triggers a profound change in myeloid cell metabolism and function. Purifying and characterizing this peptide could offer a new treatment for several diseases and prove potentially lucrative.


Subject(s)
Myeloid Cells , Peptidyl-Dipeptidase A , Animals , Humans , Peptidyl-Dipeptidase A/metabolism , Peptidyl-Dipeptidase A/genetics , Myeloid Cells/metabolism , Myeloid Cells/immunology , Myeloid Cells/drug effects , Macrophages/metabolism , Macrophages/immunology , Macrophages/drug effects , Mice , Neutrophils/immunology , Neutrophils/metabolism , Neutrophils/drug effects , Renin-Angiotensin System/drug effects , Angiotensin II/pharmacology
8.
J Biol Chem ; 300(1): 105486, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37992807

ABSTRACT

Testis angiotensin-converting enzyme (tACE) plays a critical role in male fertility, but the mechanism is unknown. By using ACE C-domain KO (CKO) mice which lack tACE activity, we found that ATP in CKO sperm was 9.4-fold lower than WT sperm. Similarly, an ACE inhibitor (ACEi) reduced ATP production in mouse sperm by 72%. Metabolic profiling showed that tACE inactivation severely affects oxidative metabolism with decreases in several Krebs cycle intermediates including citric acid, cis-aconitic acid, NAD, α-ketoglutaric acid, succinate, and L-malic acid. We found that sperms lacking tACE activity displayed lower levels of oxidative enzymes (CISY, ODO1, MDHM, QCR2, SDHA, FUMH, CPT2, and ATPA) leading to a decreased mitochondrial respiration rate. The reduced energy production in CKO sperms leads to defects in their physiological functions including motility, acrosine activity, and fertilization in vitro and in vivo. Male mice treated with ACEi show severe impairment in reproductive capacity when mated with female mice. In contrast, an angiotensin II receptor blocker (ARB) had no effect. CKO sperms express significantly less peroxisome proliferators-activated receptor gamma (PPARγ) transcription factor, and its blockade eliminates the functional differences between CKO and WT sperms, indicating PPARγ might mediate the effects of tACE on sperm metabolism. Finally, in a cohort of human volunteers, in vitro treatment with the ramipril or a PPARγ inhibitor reduced ATP production in human sperm and hence its motility and acrosine activity. These findings may have clinical significance since millions of people take ACEi daily, including men who are reproductively active.


Subject(s)
Fertilization , PPAR gamma , Peptidyl-Dipeptidase A , Spermatozoa , Animals , Female , Humans , Male , Mice , Adenosine Triphosphate/metabolism , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Fertilization/genetics , PPAR gamma/genetics , PPAR gamma/metabolism , Spermatozoa/drug effects , Spermatozoa/metabolism , Testis/enzymology , Mice, Inbred C57BL , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Mitochondrial Proteins/genetics , Gene Knockout Techniques , Oxidative Phosphorylation
9.
Nature ; 569(7756): E4, 2019 May.
Article in English | MEDLINE | ID: mdl-31043737

ABSTRACT

Further analysis has revealed that the signal reported in Extended Data Fig. 1c of this Letter is attributed to phosphorylethanolamine, not carbamoyl phosphate. A newly developed derivatization method revealed that the level of carbamoyl phosphate in these NSCLC extracts is below the detection threshold of approximately 10 nanomoles. These findings do not alter the overall conclusions of the Letter; see associated Amendment for full details. The Letter has not been corrected online.

10.
Med Res Rev ; 44(2): 587-605, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37947345

ABSTRACT

The renin-angiotensin system (RAS) has been widely known as a circulating endocrine system involved in the control of blood pressure. However, components of RAS have been found to be localized in rather unexpected sites in the body including the kidneys, brain, bone marrow, immune cells, and reproductive system. These discoveries have led to steady, growing evidence of the existence of independent tissue RAS specific to several parts of the body. It is important to understand how RAS regulates these systems for a variety of reasons: It gives a better overall picture of human physiology, helps to understand and mitigate the unintended consequences of RAS-inhibiting or activating drugs, and sets the stage for potential new therapies for a variety of ailments. This review fulfills the need for an updated overview of knowledge about local tissue RAS in several bodily systems, including their components, functions, and medical implications.


Subject(s)
Kidney , Renin-Angiotensin System , Humans , Renin-Angiotensin System/physiology , Kidney/metabolism , Angiotensin II/metabolism , Peptidyl-Dipeptidase A/metabolism
11.
J Biol Chem ; 299(1): 102749, 2023 01.
Article in English | MEDLINE | ID: mdl-36436559

ABSTRACT

The Par complex polarizes diverse animal cells through the concerted action of multiple regulators. Binding to the multi-PDZ domain containing protein Par-3 couples the complex to cortical flows that construct the Par membrane domain. Once localized properly, the complex is thought to transition from Par-3 to the Rho GTPase Cdc42 to activate the complex. While this transition is a critical step in Par-mediated polarity, little is known about how it occurs. Here, we used a biochemical reconstitution approach with purified, intact Par complex and qualitative binding assays and found that Par-3 and Cdc42 exhibit strong negative cooperativity for the Par complex. The energetic coupling arises from interactions between the second and third PDZ protein interaction domains of Par-3 and the aPKC Kinase-PBM (PDZ binding motif) that mediate the displacement of Cdc42 from the Par complex. Our results indicate that Par-3, Cdc42, Par-6, and aPKC are the minimal components that are sufficient for this transition to occur and that no external factors are required. Our findings provide the mechanistic framework for understanding a critical step in the regulation of Par complex polarization and activity.


Subject(s)
cdc42 GTP-Binding Protein , rho GTP-Binding Proteins , Animals , cdc42 GTP-Binding Protein/genetics , cdc42 GTP-Binding Protein/metabolism , Cell Polarity/physiology , rho GTP-Binding Proteins/metabolism , Humans , Nerve Tissue Proteins/metabolism
12.
Clin Infect Dis ; 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38666412

ABSTRACT

In a multi-hospital cohort study of 3392 patients, positive urinalysis parameters had poor positive predictive value for diagnosing urinary tract infection (UTI). Combined urinalysis parameters (pyuria or nitrite) performed better than pyuria alone for ruling out UTI. However, performance of all urinalysis parameters was poor in older women.

13.
Clin Infect Dis ; 78(6): 1757-1768, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38537255

ABSTRACT

INTRODUCTION: A surge of human influenza A(H7N9) cases began in 2016 in China from an antigenically distinct lineage. Data are needed about the safety and immunogenicity of 2013 and 2017 A(H7N9) inactivated influenza vaccines (IIVs) and the effects of AS03 adjuvant, prime-boost interval, and priming effects of 2013 and 2017 A(H7N9) IIVs. METHODS: Healthy adults (n = 180), ages 19-50 years, were enrolled into this partially blinded, randomized, multicenter phase 2 clinical trial. Participants were randomly assigned to 1 of 6 vaccination groups evaluating homologous versus heterologous prime-boost strategies with 2 different boost intervals (21 vs 120 days) and 2 dosages (3.75 or 15 µg of hemagglutinin) administered with or without AS03 adjuvant. Reactogenicity, safety, and immunogenicity measured by hemagglutination inhibition and neutralizing antibody titers were assessed. RESULTS: Two doses of A(H7N9) IIV were well tolerated, and no safety issues were identified. Although most participants had injection site and systemic reactogenicity, these symptoms were mostly mild to moderate in severity; injection site reactogenicity was greater in vaccination groups receiving adjuvant. Immune responses were greater after an adjuvanted second dose, and with a longer interval between prime and boost. The highest hemagglutination inhibition geometric mean titer (95% confidence interval) observed against the 2017 A(H7N9) strain was 133.4 (83.6-212.6) among participants who received homologous, adjuvanted 3.75 µg + AS03/2017 doses with delayed boost interval. CONCLUSIONS: Administering AS03 adjuvant with the second H7N9 IIV dose and extending the boost interval to 4 months resulted in higher peak antibody responses. These observations can broadly inform strategic approaches for pandemic preparedness. Clinical Trials Registration. NCT03589807.


Subject(s)
Antibodies, Viral , Immunization, Secondary , Influenza A Virus, H7N9 Subtype , Influenza Vaccines , Influenza, Human , Vaccines, Inactivated , Humans , Influenza Vaccines/immunology , Influenza Vaccines/administration & dosage , Influenza Vaccines/adverse effects , Adult , Male , Female , Middle Aged , Influenza A Virus, H7N9 Subtype/immunology , Vaccines, Inactivated/immunology , Vaccines, Inactivated/administration & dosage , Vaccines, Inactivated/adverse effects , Antibodies, Viral/blood , Influenza, Human/prevention & control , Influenza, Human/immunology , Young Adult , Immunization Schedule , Hemagglutination Inhibition Tests , United States , Immunogenicity, Vaccine , Antibodies, Neutralizing/blood , Polysorbates/administration & dosage , Polysorbates/adverse effects , alpha-Tocopherol/administration & dosage , alpha-Tocopherol/adverse effects , Squalene/administration & dosage , Squalene/adverse effects , Squalene/immunology , Healthy Volunteers , Drug Combinations , Adjuvants, Vaccine/administration & dosage , Vaccination/methods , Adjuvants, Immunologic/administration & dosage , Adjuvants, Immunologic/adverse effects
14.
Article in English | MEDLINE | ID: mdl-38954823

ABSTRACT

Crohn's disease (CD) is an inflammatory bowel disease characterized by transmural inflammation and intestinal fibrosis. Mechanisms of fibrosis in CD are not well understood. Transmural inflammation is associated with inflammatory cell infiltration, stenosis, and distention, which present mechanical stress (MS) to the bowel wall. We hypothesize that MS induces gene expression of pro-fibrotic mediators such as connective tissue growth factor (CTGF), which may contribute to fibrosis in CD. A rodent model of CD was induced by intracolonic instillation of TNBS to the distal colon. TNBS instillation induced a localized transmural inflammation (site I), with a distended colon segment (site P) proximal to site I. We detected significant fibrosis and collagen content not only in site I, but also in site P in CD rats by day 7. CTGF expression increased significantly in sites P and I, but not in the segment distal to the inflammation site. Increased CTGF expression was detected mainly in the smooth muscle cells (SMC). When rats were fed exclusively with clear liquid diet to prevent mechanical distention in colitis, expression of CTGF in sites P and I was blocked. Direct stretch led to robust expression of CTGF in colonic SMC. Treatment of CD rats with anti-CTGF antibody FG-3149 reduced fibrosis and collagen content in both sites P and I and exhibited consistent trends towards normalizing expression of collagen mRNAs. In conclusion, our studies suggest that mechanical stress, by up-regulating pro-fibrotic mediators i.e. CTGF, may play a critical role in fibrosis in CD.

15.
Ann Surg ; 2024 Jul 26.
Article in English | MEDLINE | ID: mdl-39056184

ABSTRACT

OBJECTIVE: To identify if depression, resilience, and perceived control of health are related to 2.5-year mortality and instrumental activities of daily living (IADL) decline among older adults after surgery. SUMMARY BACKGROUND DATA: The relationships of psychosocial factors with postoperative mortality and IADL decline among older adults are understudied. METHODS: We identified 3778 community-dwelling older adults in the Health and Retirement Study (HRS) with Medicare claims for surgery (mean [SD] age: 75.4 [7.8] years, 53.9% women, and 86.0% non-Hispanic White). We assessed associations of depression, resilience, and perceived control of health with 2.5-year postoperative mortality and IADL decline using cox and modified Poisson regression analyses, adjusting for sociodemographic and health variables. RESULTS: The incidence of 2.5-year postoperative mortality was 18.5% and IADL decline was 9.4%. Depression was associated with a higher incidence and adjusted hazard [95% CI] of mortality (26% vs. 16%, aHR:1.2[0.9, 1.5]), but high resilience was associated with a lower incidence and adjusted hazard of mortality (9% vs. 21%, aHR:0.6[0.5, 0.8]). Those with depression had higher incidence and adjusted relative risk [95% CI] of IADL decline (17% vs. 7%, aRR:1.6[1.2, 2.2]), but lower incidence and adjusted relative risk of IADL decline was identified for those with high resilience (4% vs. 11%, aRR:0.6[0.4, 1.0]) and high perceived control of health (7% vs. 10%, aRR:0.6[0.4, 1.0]). CONCLUSION: While depression confers greater risk of mortality and IADL decline, higher resilience and perceived control of health may be protective. Addressing psychosocial factors in the peri-operative period may improve outcomes among older adults.

16.
Ann Surg ; 2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38591223

ABSTRACT

OBJECTIVE: This qualitative study aimed to explore the psychosocial experience of older adults undergoing major elective surgery from the perspective of both the patient and family caregiver. SUMMARY BACKGROUND DATA: Older adults face unique psychological and social vulnerabilities that can increase susceptibility to poor health outcomes. How these vulnerabilities influence surgical treatment and recovery is understudied in the geriatric surgical population. METHODS: Adults aged 65 and older undergoing a high-risk major elective surgery at the University of California, San Francisco and their caregivers were recruited. Semi-structured interviews were conducted at three time points: 1-2 weeks before surgery, and at 1- and 3-months following surgery. An inductive qualitative approach was used to identify underlying themes. RESULTS: Twenty-five older adult patients (age range 65-82 years, 60% male) and 11 caregivers (age range 53-78 years, 82% female) participated. Three themes were identified. First, older surgical patients experienced significant challenges to emotional well-being both before and after surgery, which had a negative impact on recovery. Second, older adults relied on a combination of personal and social resources to navigate these challenges. Lastly, both patients and caregivers desired more resources from the healthcare system to address "the emotional piece" of surgical treatment and recovery. CONCLUSIONS: Older adults and their caregivers described multiple overlapping challenges to emotional well-being that spanned the course of the perioperative period. Our findings highlight a critical component of perioperative care with significant implications for the recovery of older surgical patients.

17.
Crit Care Med ; 52(7): e376-e389, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38597793

ABSTRACT

OBJECTIVES: Understanding the long-term effects of severe COVID-19 illness on survivors is essential for effective pandemic recovery planning. Therefore, we investigated impairments among hospitalized adults discharged to long-term acute care hospitals (LTACHs) for prolonged severe COVID-19 illness who survived 1 year. DESIGN: The Recovery After Transfer to an LTACH for COVID-19 (RAFT COVID) study was a national, multicenter, prospective longitudinal cohort study. SETTING AND PATIENTS: We included hospitalized English-speaking adults transferred to one of nine LTACHs in the United States between March 2020 and February 2021 and completed a survey. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Validated instruments for impairments and free response questions about recovering. Among 282 potentially eligible participants who provided permission to be contacted, 156 (55.3%) participated (median age, 65; 38.5% female; 61.3% in good prior health; median length of stay of 57 d; 77% mechanically ventilated for a median of 26 d; 42% had a tracheostomy). Approximately two-thirds (64%) had a persistent impairment, including physical (57%), respiratory (49%; 19% on supplemental oxygen), psychiatric (24%), and cognitive impairments (15%). Nearly half (47%) had two or more impairment types. Participants also experienced persistent debility from hospital-acquired complications, including mononeuropathies and pressure ulcers. Participants described protracted recovery, attributing improvements to exercise/rehabilitation, support, and time. While considered life-altering with 78.7% not returning to their usual health, participants expressed gratitude for recovering; 99% returned home and 60% of previously employed individuals returned to work. CONCLUSIONS: Nearly two-thirds of survivors of among the most prolonged severe COVID-19 illness had persistent impairments at 1 year that resembled post-intensive care syndrome after critical illness plus debility from hospital-acquired complications.


Subject(s)
COVID-19 , Survivors , Humans , Female , Male , Middle Aged , Survivors/statistics & numerical data , Aged , Prospective Studies , United States/epidemiology , Longitudinal Studies , Adult
18.
Bioinformatics ; 39(12)2023 12 01.
Article in English | MEDLINE | ID: mdl-38039147

ABSTRACT

MOTIVATION: statistics from genome-wide association studies enable many valuable downstream analyses that are more efficient than individual-level data analysis while also reducing privacy concerns. As growing sample sizes enable better-powered analysis of gene-environment interactions, there is a need for gene-environment interaction-specific methods that manipulate and use summary statistics. RESULTS: We introduce two tools to facilitate such analysis, with a focus on statistical models containing multiple gene-exposure and/or gene-covariate interaction terms. REGEM (RE-analysis of GEM summary statistics) uses summary statistics from a single, multi-exposure genome-wide interaction study to derive analogous sets of summary statistics with arbitrary sets of exposures and interaction covariate adjustments. METAGEM (META-analysis of GEM summary statistics) extends current fixed-effects meta-analysis models to incorporate multiple exposures from multiple studies. We demonstrate the value and efficiency of these tools by exploring alternative methods of accounting for ancestry-related population stratification in genome-wide interaction study in the UK Biobank as well as by conducting a multi-exposure genome-wide interaction study meta-analysis in cohorts from the diabetes-focused ProDiGY consortium. These programs help to maximize the value of summary statistics from diverse and complex gene-environment interaction studies. AVAILABILITY AND IMPLEMENTATION: REGEM and METAGEM are open-source projects freely available at https://github.com/large-scale-gxe-methods/REGEM and https://github.com/large-scale-gxe-methods/METAGEM.


Subject(s)
Gene-Environment Interaction , Genome-Wide Association Study , Models, Statistical , Sample Size , Data Interpretation, Statistical , Polymorphism, Single Nucleotide , Phenotype
19.
Appl Environ Microbiol ; 90(4): e0204423, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38483171

ABSTRACT

The ability of some white rot basidiomycetes to remove lignin selectively from wood indicates that low molecular weight oxidants have a role in ligninolysis. These oxidants are likely free radicals generated by fungal peroxidases from compounds in the biodegrading wood. Past work supports a role for manganese peroxidases (MnPs) in the production of ligninolytic oxidants from fungal membrane lipids. However, the fatty acid alkylperoxyl radicals initially formed during this process are not reactive enough to attack the major structures in lignin. Here, we evaluate the hypothesis that the peroxidation of fatty aldehydes might provide a source of more reactive acylperoxyl radicals. We found that Gelatoporia subvermispora produced trans-2-nonenal, trans-2-octenal, and n-hexanal (a likely metabolite of trans-2,4-decadienal) during the incipient decay of aspen wood. Fungal fatty aldehydes supported the in vitro oxidation by MnPs of a nonphenolic lignin model dimer, and also of the monomeric model veratryl alcohol. Experiments with the latter compound showed that the reactions were partially inhibited by oxalate, the chelator that white rot fungi employ to detach Mn3+ from the MnP active site, but nevertheless proceeded at its physiological concentration of 1 mM. The addition of catalase was inhibitory, which suggests that the standard MnP catalytic cycle is involved in the oxidation of aldehydes. MnP oxidized trans-2-nonenal quantitatively to trans-2-nonenoic acid with the consumption of one O2 equivalent. The data suggest that when Mn3+ remains associated with MnP, it can oxidize aldehydes to their acyl radicals, and the latter subsequently add O2 to become ligninolytic acylperoxyl radicals.IMPORTANCEThe biodegradation of lignin by white rot fungi is essential for the natural recycling of plant biomass and has useful applications in lignocellulose bioprocessing. Although fungal peroxidases have a key role in ligninolysis, past work indicates that biodegradation is initiated by smaller, as yet unidentified oxidants that can infiltrate the substrate. Here, we present evidence that the peroxidase-catalyzed oxidation of naturally occurring fungal aldehydes may provide a source of ligninolytic free radical oxidants.


Subject(s)
Basidiomycota , Manganese , Polyporales , Lignin/metabolism , Fungal Proteins/metabolism , Basidiomycota/metabolism , Aldehydes , Peroxidases/metabolism , Fatty Acids , Oxidants
20.
J Urol ; 211(5): 690-698, 2024 May.
Article in English | MEDLINE | ID: mdl-38330392

ABSTRACT

PURPOSE: Patients with suspected UTIs are categorized into 3 clinical phenotypes based on current guidelines: no UTI, asymptomatic bacteriuria (ASB), or UTI. However, all patients may not fit neatly into these groups. Our objective was to characterize clinical presentations of patients who receive urine tests using the "continuum of UTI" approach. MATERIALS AND METHODS: This was a retrospective cohort study of a random sample of adult noncatheterized inpatient and emergency department encounters with paired urinalysis and urine cultures from 5 hospitals in 3 states between January 01, 2017, and December 31, 2019. Trained abstractors collected clinical (eg, symptom) and demographic data. A focus group discussion with multidisciplinary experts was conducted to define the continuum of UTI, a 5-level classification scheme that includes 2 new categories: lower urinary tract symptoms/other urologic symptoms and bacteriuria of unclear significance. The newly defined continuum of UTI categories were compared to the current UTI classification scheme. RESULTS: Of 220,531 encounters, 3392 randomly selected encounters were reviewed. Based on the current classification scheme, 32.1% (n = 704) had ASB and 53% (n = 1614) did not have a UTI. When applying the continuum of UTI categories, 68% of patients (n = 478) with ASB were reclassified as bacteriuria of unclear significance and 29% of patients (n = 467) with "no UTI" were reclassified to lower urinary tract symptoms/other urologic symptoms. CONCLUSIONS: Our data suggest the need to reframe our conceptual model of UTI vs ASB to reflect the full spectrum of clinical presentations, acknowledge the diagnostic uncertainty faced by frontline clinicians, and promote a nuanced approach to diagnosis and management of UTIs.


Subject(s)
Bacteriuria , Lower Urinary Tract Symptoms , Urinary Tract Infections , Adult , Humans , Bacteriuria/diagnosis , Bacteriuria/drug therapy , Retrospective Studies , Urinary Tract Infections/diagnosis , Urinary Tract Infections/drug therapy , Urinalysis , Lower Urinary Tract Symptoms/drug therapy , Anti-Bacterial Agents/therapeutic use
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