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1.
Eur Heart J ; 2024 May 17.
Artigo em Inglês | MEDLINE | ID: mdl-38757788

RESUMO

BACKGROUND AND AIMS: Incident heart failure (HF) among individuals with chronic kidney disease (CKD) incurs hospitalizations that burden patients and health care systems. There are few preventative therapies, and the Pooled Cohort equations to Prevent Heart Failure (PCP-HF) perform poorly in the setting of CKD. New drug targets and better risk stratification are urgently needed. METHODS: In this analysis of incident HF, SomaScan V4.0 (4638 proteins) was analysed in 2906 participants of the Chronic Renal Insufficiency Cohort (CRIC) with validation in the Atherosclerosis Risk in Communities (ARIC) study. The primary outcome was 14-year incident HF (390 events); secondary outcomes included 4-year HF (183 events), HF with reduced ejection fraction (137 events), and HF with preserved ejection fraction (165 events). Mendelian randomization and Gene Ontology were applied to examine causality and pathways. The performance of novel multi-protein risk models was compared to the PCP-HF risk score. RESULTS: Over 200 proteins were associated with incident HF after adjustment for estimated glomerular filtration rate at P < 1 × 10-5. After adjustment for covariates including N-terminal pro-B-type natriuretic peptide, 17 proteins remained associated at P < 1 × 10-5. Mendelian randomization associations were found for six proteins, of which four are druggable targets: FCG2B, IGFBP3, CAH6, and ASGR1. For the primary outcome, the C-statistic (95% confidence interval [CI]) for the 48-protein model in CRIC was 0.790 (0.735, 0.844) vs. 0.703 (0.644, 0.762) for the PCP-HF model (P = .001). C-statistic (95% CI) for the protein model in ARIC was 0.747 (0.707, 0.787). CONCLUSIONS: Large-scale proteomics reveal novel circulating protein biomarkers and potential mediators of HF in CKD. Proteomic risk models improve upon the PCP-HF risk score in this population.

2.
PLoS One ; 19(4): e0299332, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38652731

RESUMO

Standard race adjustments for estimating glomerular filtration rate (GFR) and reference creatinine can yield a lower acute kidney injury (AKI) and chronic kidney disease (CKD) prevalence among African American patients than non-race adjusted estimates. We developed two race-agnostic computable phenotypes that assess kidney health among 139,152 subjects admitted to the University of Florida Health between 1/2012-8/2019 by removing the race modifier from the estimated GFR and estimated creatinine formula used by the race-adjusted algorithm (race-agnostic algorithm 1) and by utilizing 2021 CKD-EPI refit without race formula (race-agnostic algorithm 2) for calculations of the estimated GFR and estimated creatinine. We compared results using these algorithms to the race-adjusted algorithm in African American patients. Using clinical adjudication, we validated race-agnostic computable phenotypes developed for preadmission CKD and AKI presence on 300 cases. Race adjustment reclassified 2,113 (8%) to no CKD and 7,901 (29%) to a less severe CKD stage compared to race-agnostic algorithm 1 and reclassified 1,208 (5%) to no CKD and 4,606 (18%) to a less severe CKD stage compared to race-agnostic algorithm 2. Of 12,451 AKI encounters based on race-agnostic algorithm 1, race adjustment reclassified 591 to No AKI and 305 to a less severe AKI stage. Of 12,251 AKI encounters based on race-agnostic algorithm 2, race adjustment reclassified 382 to No AKI and 196 (1.6%) to a less severe AKI stage. The phenotyping algorithm based on refit without race formula performed well in identifying patients with CKD and AKI with a sensitivity of 100% (95% confidence interval [CI] 97%-100%) and 99% (95% CI 97%-100%) and a specificity of 88% (95% CI 82%-93%) and 98% (95% CI 93%-100%), respectively. Race-agnostic algorithms identified substantial proportions of additional patients with CKD and AKI compared to race-adjusted algorithm in African American patients. The phenotyping algorithm is promising in identifying patients with kidney disease and improving clinical decision-making.


Assuntos
Injúria Renal Aguda , Negro ou Afro-Americano , Taxa de Filtração Glomerular , Hospitalização , Insuficiência Renal Crônica , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Injúria Renal Aguda/diagnóstico , Injúria Renal Aguda/epidemiologia , Algoritmos , Creatinina/sangue , Rim/fisiopatologia , Fenótipo , Insuficiência Renal Crônica/fisiopatologia , Insuficiência Renal Crônica/epidemiologia , Insuficiência Renal Crônica/diagnóstico
3.
JAMA Intern Med ; 184(4): 451-452, 2024 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-38372980
4.
PLoS One ; 18(12): e0293945, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38079395

RESUMO

BACKGROUND: Patients with kidney failure suffer high mortality, and we currently lack markers for risk stratification for these patients. We carried out a quality control study of a modified aptamer assay (SomaScan v.4.0) that measures ~ 5000 proteins, in preparation for a larger study using this platform in cohorts with kidney failure. METHODS: Forty participants from the Cardiac, Endothelial Function and Arterial Stiffness in End-Stage Renal Disease (CERES study) were selected to analyze technical and short-term biological variability, orthogonal correlations and differential protein expression in plasma from patients who died during 2.5 year follow-up. Long-term (one year) variability was studied in 421 participants in the Chronic Renal Insufficiency Cohort. We evaluated 4849 aptamers (4607 unique proteins) using data formats including raw data and data formatted using Adaptive Normalization by Maximum Likelihood (ANML), an algorithm developed for SomaScan data in individuals with normal kidney function. RESULTS: In ANML format, median[IQR] intra-assay coefficient of variation (CV) was 2.38%[1.76, 3.40] and inter-assay CV was 7.38%[4.61, 13.12]. Short-term within-subject CV was 5.76% [3.35, 9.72]; long-term CV was 8.71%[5.91, 13.37]. Spearman correlations between aptamer and traditional assays for PTH, NT-proBNP, FGF-23 and CRP were all > 0.7. Fold-change (FC) in protein levels among non-survivors, significant after Bonferroni correction, included SVEP1 (FC[95% CI] 2.14 [1.62, 2.82]), keratocan (1.74 [1.40, 2.15]) and LanC-like protein 1 (0.56 [0.45, 0.70]). Compared to raw aptamer data, technical and short-term biological variability in paired samples was lower in ANML-formatted data. ANML formatting had minimal impact on orthogonal correlations with traditional assays or the associations of proteins with the phenotype of mortality. CONCLUSIONS: SomaScan had excellent technical variability and low within-subject short-term variability. ANML formatting could facilitate comparison of biomarker results with other studies that utilize this format. We expect SomaScan to provide novel and reproducible information in patients with kidney failure on dialysis.


Assuntos
Falência Renal Crônica , Diálise Renal , Humanos , Proteômica/métodos , Falência Renal Crônica/terapia , Biomarcadores , Oligonucleotídeos
5.
Nat Commun ; 14(1): 6340, 2023 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-37816758

RESUMO

Progression of chronic kidney disease (CKD) portends myriad complications, including kidney failure. In this study, we analyze associations of 4638 plasma proteins among 3235 participants of the Chronic Renal Insufficiency Cohort Study with the primary outcome of 50% decline in estimated glomerular filtration rate or kidney failure over 10 years. We validate key findings in the Atherosclerosis Risk in the Communities study. We identify 100 circulating proteins that are associated with the primary outcome after multivariable adjustment, using a Bonferroni statistical threshold of significance. Individual protein associations and biological pathway analyses highlight the roles of bone morphogenetic proteins, ephrin signaling, and prothrombin activation. A 65-protein risk model for the primary outcome has excellent discrimination (C-statistic[95%CI] 0.862 [0.835, 0.889]), and 14/65 proteins are druggable targets. Potentially causal associations for five proteins, to our knowledge not previously reported, are supported by Mendelian randomization: EGFL9, LRP-11, MXRA7, IL-1 sRII and ILT-2. Modifiable protein risk markers can guide therapeutic drug development aimed at slowing CKD progression.


Assuntos
Insuficiência Renal Crônica , Insuficiência Renal , Humanos , Estudos de Coortes , Proteômica , Estudos Prospectivos , Insuficiência Renal Crônica/metabolismo , Insuficiência Renal/complicações , Progressão da Doença
6.
Front Nutr ; 10: 1179295, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37457968

RESUMO

Background: Fiber is a potential therapeutic to suppress microbiota-generated uremic molecules. This study aimed to determine if fiber supplementation decreased serum levels of uremic molecules through the modulation of gut microbiota in adults undergoing hemodialysis. Methods: A randomized, double-blinded, controlled crossover study was conducted. Following a 1-week baseline, participants consumed muffins with added pea hull fiber (PHF) (15 g/d) and control muffins daily, each for 4 weeks, separated by a 4-week washout. Blood and stool samples were collected per period. Serum p-cresyl sulfate (PCS), indoxyl sulfate (IS), phenylacetylglutamine (PAG), and trimethylamine N-oxide (TMAO) were quantified by LC-MS/MS, and fecal microbiota profiled by 16S rRNA gene amplicon sequencing and specific taxa of interest by qPCR. QIIME 2 sample-classifier was used to discover unique microbiota profiles due to the consumption of PHF. Results: Intake of PHF contributed an additional 9 g/d of dietary fiber to the subjects' diet due to compliance. No significant changes from baseline were observed in serum PCS, IS, PAG, or TMAO, or for the relative quantification of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium, or Roseburia, taxa considered health-enhancing. Dietary protein intake and IS (r = -0.5, p = 0.05) and slow transit stool form and PCS (r = 0.7, p < 0.01) were significantly correlated at baseline. PHF and control periods were not differentiated; however, using machine learning, taxa most distinguishing the microbiota composition during the PHF periods compared to usual diet alone were enriched Gemmiger, Collinsella, and depleted Lactobacillus, Ruminococcus, Coprococcus, and Mogibacteriaceae. Conclusion: PHF supplementation did not mitigate serum levels of targeted microbial-generated uremic molecules. Given the high cellulose content, which may be resistant to fermentation, PHF may not exert sufficient effects on microbiota composition to modulate its activity at the dose consumed.

7.
Eur Heart J ; 44(23): 2095-2110, 2023 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-37014015

RESUMO

AIMS: Chronic kidney disease (CKD) is widely prevalent and independently increases cardiovascular risk. Cardiovascular risk prediction tools derived in the general population perform poorly in CKD. Through large-scale proteomics discovery, this study aimed to create more accurate cardiovascular risk models. METHODS AND RESULTS: Elastic net regression was used to derive a proteomic risk model for incident cardiovascular risk in 2182 participants from the Chronic Renal Insufficiency Cohort. The model was then validated in 485 participants from the Atherosclerosis Risk in Communities cohort. All participants had CKD and no history of cardiovascular disease at study baseline when ∼5000 proteins were measured. The proteomic risk model, which consisted of 32 proteins, was superior to both the 2013 ACC/AHA Pooled Cohort Equation and a modified Pooled Cohort Equation that included estimated glomerular filtrate rate. The Chronic Renal Insufficiency Cohort internal validation set demonstrated annualized receiver operating characteristic area under the curve values from 1 to 10 years ranging between 0.84 and 0.89 for the protein and 0.70 and 0.73 for the clinical models. Similar findings were observed in the Atherosclerosis Risk in Communities validation cohort. For nearly half of the individual proteins independently associated with cardiovascular risk, Mendelian randomization suggested a causal link to cardiovascular events or risk factors. Pathway analyses revealed enrichment of proteins involved in immunologic function, vascular and neuronal development, and hepatic fibrosis. CONCLUSION: In two sizeable populations with CKD, a proteomic risk model for incident cardiovascular disease surpassed clinical risk models recommended in clinical practice, even after including estimated glomerular filtration rate. New biological insights may prioritize the development of therapeutic strategies for cardiovascular risk reduction in the CKD population.


Assuntos
Aterosclerose , Doenças Cardiovasculares , Insuficiência Renal Crônica , Humanos , Doenças Cardiovasculares/etiologia , Doenças Cardiovasculares/complicações , Fatores de Risco , Proteômica , Insuficiência Renal Crônica/complicações , Insuficiência Renal Crônica/epidemiologia , Medição de Risco , Aterosclerose/complicações , Taxa de Filtração Glomerular/fisiologia , Fatores de Risco de Doenças Cardíacas
9.
BMC Bioinformatics ; 24(1): 64, 2023 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-36829114

RESUMO

BACKGROUND: Methods for inferring the three-dimensional (3D) configuration of chromatin from conformation capture assays that provide strictly pairwise interactions, notably Hi-C, utilize the attendant contact matrix as input. More recent assays, in particular split-pool recognition of interactions by tag extension (SPRITE), capture multi-way interactions instead of solely pairwise contacts. These assays yield contacts that straddle appreciably greater genomic distances than Hi-C, in addition to instances of exceptionally high-order chromatin interaction. Such attributes are anticipated to be consequential with respect to 3D genome reconstruction, a task yet to be undertaken with multi-way contact data. However, performing such 3D reconstruction using distance-based reconstruction techniques requires framing multi-way contacts as (pairwise) distances. Comparing approaches for so doing, and assessing the resultant impact of long-range and multi-way contacts, are the objectives of this study. RESULTS: We obtained 3D reconstructions via multi-dimensional scaling under a variety of weighting schemes for mapping SPRITE multi-way contacts to pairwise distances. Resultant configurations were compared following Procrustes alignment and relationships were assessed between associated Procrustes root mean square errors and key features such as the extent of multi-way and/or long-range contacts. We found that these features had surprisingly limited influence on 3D reconstruction, a finding we attribute to their influence being diminished by the preponderance of pairwise contacts. CONCLUSION: Distance-based 3D genome reconstruction using SPRITE multi-way contact data is not appreciably affected by the weighting scheme used to convert multi-way interactions to pairwise distances.


Assuntos
Cromatina , Cromossomos , Genoma , Genômica/métodos , Conformação Molecular
10.
J Appl Lab Med ; 8(3): 491-503, 2023 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-36705086

RESUMO

BACKGROUND: We carried out a study of the aptamer proteomic assay, SomaScan V4, to evaluate the analytical and biological variability of the assay in plasma samples of patients with moderate to severe chronic kidney disease (CKD). METHODS: Plasma samples were selected from 2 sources: (a) 24 participants from the Chronic Renal Insufficiency Cohort (CRIC) and (b) 49 patients from the Brigham and Women's Hospital-Kidney/Renal Clinic. We calculated intra-assay variability from both sources and examined short-term biological variability in samples from the Brigham clinic. We also measured correlations of aptamer measurements with traditional biomarker assays. RESULTS: A total of 4656 unique proteins (4849 total aptamer measures) were analyzed in all samples. Median (interquartile range [IQR] intra-assay CV) was 3.7% (2.8-5.3) in CRIC and 5.0% (3.8-7.0) in Brigham samples. Median (IQR) biological CV among Brigham samples drawn from one individual on 2 occasions separated by median (IQR) 7 (4-14) days was 8.7% (6.2-14). CVs were independent of CKD stage, diabetes, or albuminuria but were higher in patients with systemic lupus erythematosus. Rho correlations between aptamer and traditional assays for biomarkers of interest were cystatin C = 0.942, kidney injury model-1 = 0.905, fibroblast growth factor-23 = 0.541, tumor necrosis factor receptors 1 = 0.781 and 2 = 0.843, P < 10-100 for all. CONCLUSIONS: Intra-assay and within-subject variability for SomaScan in the CKD setting was low and similar to assay variability reported from individuals without CKD. Intra-assay precision was excellent whether samples were collected in an optimal research protocol, as were CRIC samples, or in the clinical setting, as were the Brigham samples.


Assuntos
Diabetes Mellitus , Insuficiência Renal Crônica , Humanos , Feminino , Proteômica , Estudos de Coortes , Insuficiência Renal Crônica/diagnóstico , Biomarcadores
11.
Clin Immunol ; 248: 109213, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-36566913

RESUMO

Ferroptosis is a druggable, iron-dependent form of cell death that is characterized by lipid peroxidation but has received little attention in lupus nephritis. Kidneys of lupus nephritis patients and mice showed increased lipid peroxidation mainly in the tubular segments and an increase in Acyl-CoA synthetase long-chain family member 4, a pro-ferroptosis enzyme. Nephritic mice had an attenuated expression of SLC7A11, a cystine importer, an impaired glutathione synthesis pathway, and low expression of glutathione peroxidase 4, a ferroptosis inhibitor. Lipidomics of nephritic kidneys confirmed ferroptosis. Using nephrotoxic serum, we induced immune complex glomerulonephritis in congenic mice and demonstrate that impaired iron sequestration within the proximal tubules exacerbates ferroptosis. Lupus nephritis patient serum rendered human proximal tubular cells susceptibility to ferroptosis which was inhibited by Liproxstatin-2, a novel ferroptosis inhibitor. Collectively, our findings identify intra-renal ferroptosis as a pathological feature and contributor to tubular injury in human and murine lupus nephritis.


Assuntos
Ferroptose , Nefropatias , Nefrite Lúpica , Humanos , Camundongos , Animais , Ferro/metabolismo , Glomérulos Renais/metabolismo , Células Epiteliais/metabolismo
13.
Vasc Endovascular Surg ; 57(4): 357-364, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36541126

RESUMO

BACKGROUND: Chronic limb-threatening ischemia (CLTI) can be associated with dismal outcomes but there are limited real-world data to further define the impact of end-stage kidney disease (ESKD) on outcomes nationally in this subset of patients. We sought to characterize national patterns of inpatient treatment of CLTI and compare outcomes in patients without ESKD. METHODS: The National Inpatient Sample was queried from 2015-2018 for all hospital admissions including treatment for CLTI. Mixed-effects linear and logistic regression models were used to estimate the effect of ESKD on outcomes and treatment choice. RESULTS: We identified 11 652 hospital admissions with CLTI alone and 2705 with CLTI + ESKD. Hospital admissions with CLTI + ESKD patients included patients who were younger (66 vs 69 years, P < .0001), less likely to be white (39% vs 63%, P < .0001), and more likely to reside in lower income large metropolitan areas. Admissions for CLTI + ESKD patients had a lower likelihood of open arterial reconstruction (OR .40, P < .0001) and a higher likelihood of endovascular revascularization or major limb amputation (OR 1.70, P < .0001). Admissions for CLTI + ESKD also had a 4.5- and 1.5-fold higher odds of in-hospital death and complications. These findings were associated with a longer LOS (P < .0001), increased probability of discharge to rehabilitation facility (50% vs 41%, P < .0001), and greater hospital charges (median, $107 K vs $85 K, P < .0001). CONCLUSIONS: Compared to hospital admissions for patients without ESKD, admissions for patients with CLTI + ESKD demonstrated distinctive demographic characteristics, a lower likelihood of open revascularization and a higher likelihood of endovascular revascularization and major limb amputation. Chronic limb-threatening ischemia + ESKD hospital admissions showed worse overall outcomes and greater resource utilization compared to CLTI admissions without ESKD.


Assuntos
Procedimentos Endovasculares , Falência Renal Crônica , Doença Arterial Periférica , Humanos , Isquemia Crônica Crítica de Membro , Fatores de Risco , Mortalidade Hospitalar , Procedimentos Endovasculares/efeitos adversos , Resultado do Tratamento , Doença Crônica , Salvamento de Membro , Doença Arterial Periférica/diagnóstico , Doença Arterial Periférica/terapia , Isquemia/diagnóstico , Isquemia/cirurgia , Falência Renal Crônica/diagnóstico , Falência Renal Crônica/epidemiologia , Falência Renal Crônica/terapia , Estudos Retrospectivos
14.
Biostatistics ; 24(3): 618-634, 2023 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-34494087

RESUMO

Three-dimensional (3D) genome architecture is critical for numerous cellular processes, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Inferring 3D chromatin configurations has been advanced by the emergence of chromatin conformation capture assays, notably Hi-C, and attendant 3D reconstruction algorithms. These have enhanced understanding of chromatin spatial organization and afforded numerous downstream biological insights. Until recently, comparisons of 3D reconstructions between conditions and/or cell types were limited to prescribed structural features. However, multiMDS, a pioneering approach developed by Rieber and Mahony (2019). that performs joint reconstruction and alignment, enables quantification of all locus-specific differences between paired Hi-C data sets. By subsequently mapping these differences to the linear (1D) genome the identification of relocalization regions is facilitated through the use of peak calling in conjunction with continuous wavelet transformation. Here, we seek to refine this approach by performing the search for significant relocalization regions in terms of the 3D structures themselves, thereby retaining the benefits of 3D reconstruction and avoiding limitations associated with the 1D perspective. The search for (extreme) relocalization regions is conducted using the patient rule induction method (PRIM). Considerations surrounding orienting structures with respect to compartmental and principal component axes are discussed, as are approaches to inference and reconstruction accuracy assessment. The illustration makes recourse to comparisons between four different cell types.


Assuntos
Cromatina , Genoma , Humanos , Cromatina/genética , Conformação Molecular , Algoritmos
17.
Shock ; 58(1): 20-27, 2022 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-35904146

RESUMO

ABSTRACT: Objective: The aim of this study was to characterize early urinary gene expression differences between patients with sepsis and patients with sterile inflammation and summarize in terms of a reproducible sepsis probability score. Design: This was a prospective observational cohort study. Setting: The study was conducted in a quaternary care academic hospital. Patients: One hundred eighty-six sepsis patients and 78 systemic inflammatory response syndrome (SIRS) patients enrolled between January 2015 and February 2018. Interventions: Whole-genome transcriptomic analysis of RNA was extracted from urine obtained from sepsis patients within 12 hours of sepsis onset and from patients with surgery-acquired SIRS within 4 hours after major inpatient surgery. Measurements and Main Results: We identified 422 of 23,956 genes (1.7%) that were differentially expressed between sepsis and SIRS patients. Differentially expressed probes were provided to a collection of machine learning feature selection models to identify focused probe sets that differentiate between sepsis and SIRS. These probe sets were combined to find an optimal probe set (UrSepsisModel) and calculate a urinary sepsis score (UrSepsisScore), which is the geometric mean of downregulated genes subtracted from the geometric mean of upregulated genes. This approach summarizes the expression values of all decisive genes as a single sepsis score. The UrSepsisModel and UrSepsisScore achieved area under the receiver operating characteristic curves 0.91 (95% confidence interval, 0.86-0.96) and 0.80 (95% confidence interval, 0.70-0.88) on the validation cohort, respectively. Functional analyses of probes associated with sepsis demonstrated metabolic dysregulation manifest as reduced oxidative phosphorylation, decreased amino acid metabolism, and decreased oxidation of lipids and fatty acids. Conclusions: Whole-genome transcriptomic profiling of urinary cells revealed focused probe panels that can function as an early diagnostic tool for differentiating sepsis from sterile SIRS. Functional analysis of differentially expressed genes demonstrated a distinct metabolic dysregulation signature in sepsis.


Assuntos
Sepse , Perfilação da Expressão Gênica , Humanos , Inflamação/genética , Estudos Prospectivos , Sepse/diagnóstico , Sepse/genética , Síndrome de Resposta Inflamatória Sistêmica/diagnóstico , Síndrome de Resposta Inflamatória Sistêmica/genética
18.
NAR Genom Bioinform ; 4(2): lqac038, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35571676

RESUMO

The three-dimensional (3D) configuration of chromatin impacts numerous cellular processes. However, directly observing chromatin architecture at high resolution is challenging. Accordingly, inferring 3D structure utilizing chromatin conformation capture assays, notably Hi-C, has received considerable attention, with a multitude of reconstruction algorithms advanced. While these have enhanced appreciation of chromatin organization, most suffer from a serious shortcoming when faced with diploid genomes: inability to disambiguate contacts between corresponding loci on homologous chromosomes, making attendant reconstructions potentially meaningless. Three recent proposals offer a computational way forward at the expense of strong assumptions. Here, we show that making plausible assumptions about the components of homologous chromosome contacts provides a basis for rescuing conventional consensus-based, unphased reconstruction. This would be consequential since not only are assumptions needed for diploid reconstruction considerable, but the sophistication of select unphased algorithms affords substantive advantages with regard resolution and folding complexity. Rather than presuming that the requisite salvaging assumptions are met, we exploit a recent imaging technology, in situ genome sequencing (IGS), to comprehensively evaluate their reasonableness. We analogously use IGS to assess assumptions underpinning diploid reconstruction algorithms. Results convincingly demonstrate that, in all instances, assumptions are not met, making further algorithm development, potentially informed by IGS data, essential.

19.
J Surg Res ; 277: 372-383, 2022 09.
Artigo em Inglês | MEDLINE | ID: mdl-35569215

RESUMO

INTRODUCTION: Sepsis has complex, time-sensitive pathophysiology and important phenotypic subgroups. The objective of this study was to use machine learning analyses of blood and urine biomarker profiles to elucidate the pathophysiologic signatures of subgroups of surgical sepsis patients. METHODS: This prospective cohort study included 243 surgical sepsis patients admitted to a quaternary care center between January 2015 and June 2017. We applied hierarchical clustering to clinical variables and 42 blood and urine biomarkers to identify phenotypic subgroups in a development cohort. Clinical characteristics and short-term and long-term outcomes were compared between clusters. A naïve Bayes classifier predicted cluster labels in a validation cohort. RESULTS: The development cohort contained one cluster characterized by early organ dysfunction (cluster I, n = 18) and one cluster characterized by recovery (cluster II, n = 139). Cluster I was associated with higher Acute Physiologic Assessment and Chronic Health Evaluation II (30 versus 16, P < 0.001) and SOFA scores (13 versus 5, P < 0.001), greater prevalence of chronic cardiovascular and renal disease (P < 0.001) and septic shock (78% versus 17%, P < 0.001). Cluster I had higher mortality within 14 d of sepsis onset (11% versus 1.5%, P = 0.001) and within 1 y (44% versus 20%, P = 0.032), and higher incidence of chronic critical illness (61% versus 30%, P = 0.001). The Bayes classifier achieved 95% accuracy and identified two clusters that were similar to development cohort clusters. CONCLUSIONS: Machine learning analyses of clinical and biomarker variables identified an early organ dysfunction sepsis phenotype characterized by inflammation, renal dysfunction, endotheliopathy, and immunosuppression, as well as poor short-term and long-term clinical outcomes.


Assuntos
Insuficiência de Múltiplos Órgãos , Sepse , Teorema de Bayes , Biomarcadores , Mortalidade Hospitalar , Humanos , Escores de Disfunção Orgânica , Estudos Prospectivos , Sepse/diagnóstico , Sepse/epidemiologia , Sepse/etiologia
20.
Kidney360 ; 3(1): 91-98, 2022 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-35368570

RESUMO

Background: Pre-ESKD Kidney Disease Education (KDE) has been shown to improve multiple CKD outcomes, but its effect on vascular access outcomes is not well studied. In 2010, Medicare launched KDE reimbursements policy for patients with advanced CKD. Methods: In this retrospective USRDS analysis, we identified all adult patients on incident hemodialysis with ≥6 months of pre-ESKD Medicare coverage during the first 5 years of CMS-KDE policy and divided them into CMS-KDE services recipients (KDE cohort) and nonrecipients (non-KDE cohort). The primary outcome was incident arteriovenous fistula (AVF) and the composite of incident AVF or arteriovenous graft (AVG) utilization. Secondary outcomes were central venous catheter (CVC) with maturing AVF/AVG and pure CVC utilizations. Step-wise multivariate analyses were performed in four progressive models (model 1, KDE alone; model 2, multivariate model encompassing model 1 with sociodemographics; model 3, model 2 with comorbidity and functional status; and model 4, model 3 with pre-ESKD nephrology care). Results: Of the 211,990 qualifying patients on incident hemodialysis during the study period, 2887 (1%) received KDE services before dialysis initiation. The rates of incident AVF and composite AVF/AVG were more than double (30% and 35%, respectively, compared with 14% and 17%), and pure catheter use about a third lower (40% compared with 65%) in the KDE cohort compared with the non-KDE cohort. The maximally adjusted odds ratios in model 4 for study outcomes were incident AVF use, 1.78, 99% confidence interval, 1.55 to 2.05; incident AVF/AVG use, 1.78, 99% confidence interval, 1.56 to 2.03; incident CVC with maturing AVF/AVG, 1.69, 99% confidence interval, 1.44 to 1.97; and pure CVC without any AVF/AVG, 0.51, 99% confidence interval, 0.45 to 0.58. The benefits of the KDE service were maintained even after accounting for the presence, duration, and facility of ESKD care. Conclusion: The occurrence of pre-ESRD KDE service is associated with significantly improved incident vascular access outcomes. Targeted studies are needed to examine the effect of KDE on patient engagement and self-efficacy as a cause for improvement in vascular access outcomes.


Assuntos
Derivação Arteriovenosa Cirúrgica , Cateteres Venosos Centrais , Falência Renal Crônica , Adulto , Idoso , Derivação Arteriovenosa Cirúrgica/efeitos adversos , Cateteres Venosos Centrais/efeitos adversos , Humanos , Falência Renal Crônica/epidemiologia , Medicare , Diálise Renal/efeitos adversos , Estudos Retrospectivos , Estados Unidos/epidemiologia
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