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1.
Plant Cell ; 36(4): 812-828, 2024 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-38231860

RESUMEN

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.


Asunto(s)
Perfilación de la Expresión Génica , Plantas , Reproducibilidad de los Resultados , Plantas/genética , Estrés Fisiológico/genética , Almacenamiento y Recuperación de la Información
2.
Brief Bioinform ; 25(3)2024 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-38581421

RESUMEN

Boolean models of gene regulatory networks (GRNs) have gained widespread traction as they can easily recapitulate cellular phenotypes via their attractor states. Their overall dynamics are embodied in a state transition graph (STG). Indeed, two Boolean networks (BNs) with the same network structure and attractors can have drastically different STGs depending on the type of Boolean functions (BFs) employed. Our objective here is to systematically delineate the effects of different classes of BFs on the structural features of the STG of reconstructed Boolean GRNs while keeping network structure and biological attractors fixed, and explore the characteristics of BFs that drive those features. Using $10$ reconstructed Boolean GRNs, we generate ensembles that differ in BFs and compute from their STGs the dynamics' rate of contraction or 'bushiness' and rate of 'convergence', quantified with measures inspired from cellular automata (CA) that are based on the garden-of-Eden (GoE) states. We find that biologically meaningful BFs lead to higher STG 'bushiness' and 'convergence' than random ones. Obtaining such 'global' measures gets computationally expensive with larger network sizes, stressing the need for feasible proxies. So we adapt Wuensche's $Z$-parameter in CA to BFs in BNs and provide four natural variants, which, along with the average sensitivity of BFs computed at the network level, comprise our descriptors of local dynamics and we find some of them to be good proxies for bushiness. Finally, we provide an excellent proxy for the 'convergence' based on computing transient lengths originating at random states rather than GoE states.


Asunto(s)
Algoritmos , Modelos Genéticos , Redes Reguladoras de Genes , Autómata Celular
3.
Brief Bioinform ; 24(3)2023 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-37114653

RESUMEN

Boolean models are a well-established framework to model developmental gene regulatory networks (DGRNs) for acquisition of cellular identities. During the reconstruction of Boolean DGRNs, even if the network structure is given, there is generally a large number of combinations of Boolean functions that will reproduce the different cell fates (biological attractors). Here we leverage the developmental landscape to enable model selection on such ensembles using the relative stability of the attractors. First we show that previously proposed measures of relative stability are strongly correlated and we stress the usefulness of the one that captures best the cell state transitions via the mean first passage time (MFPT) as it also allows the construction of a cellular lineage tree. A property of great computational importance is the insensitivity of the different stability measures to changes in noise intensities. That allows us to use stochastic approaches to estimate the MFPT and thereby scale up the computations to large networks. Given this methodology, we revisit different Boolean models of Arabidopsis thaliana root development, showing that a most recent one does not respect the biologically expected hierarchy of cell states based on relative stabilities. We therefore developed an iterative greedy algorithm that searches for models which satisfy the expected hierarchy of cell states and found that its application to the root development model yields many models that meet this expectation. Our methodology thus provides new tools that can enable reconstruction of more realistic and accurate Boolean models of DGRNs.


Asunto(s)
Arabidopsis , Redes Reguladoras de Genes , Modelos Genéticos , Algoritmos , Diferenciación Celular , Arabidopsis/genética
4.
Eur Heart J ; 45(32): 2954-2964, 2024 Aug 21.
Artículo en Inglés | MEDLINE | ID: mdl-38733175

RESUMEN

BACKGROUND AND AIMS: In patients with chronic heart failure (HF), the MONITOR-HF trial demonstrated the efficacy of pulmonary artery (PA)-guided HF therapy over standard of care in improving quality of life and reducing HF hospitalizations and mean PA pressure. This study aimed to evaluate the consistency of these benefits in relation to clinically relevant subgroups. METHODS: The effect of PA-guided HF therapy was evaluated in the MONITOR-HF trial among predefined subgroups based on age, sex, atrial fibrillation, diabetes mellitus, left ventricular ejection fraction, HF aetiology, cardiac resynchronization therapy, and implantable cardioverter defibrillator. Outcome measures were based upon significance in the main trial and included quality of life-, clinical-, and PA pressure endpoints, and were assessed for each subgroup. Differential effects in relation to the subgroups were assessed with interaction terms. Both unadjusted and multiple testing adjusted interaction terms were presented. RESULTS: The effects of PA monitoring on quality of life, clinical events, and PA pressure were consistent in the predefined subgroups, without any clinically relevant heterogeneity within or across all endpoint categories (all adjusted interaction P-values were non-significant). In the unadjusted analysis of the primary endpoint quality-of-life change, weak trends towards a less pronounced effect in older patients (Pinteraction = .03; adjusted Pinteraction = .33) and diabetics (Pinteraction = .01; adjusted Pinteraction = .06) were observed. However, these interaction effects did not persist after adjusting for multiple testing. CONCLUSIONS: This subgroup analysis confirmed the consistent benefits of PA-guided HF therapy observed in the MONITOR-HF trial across clinically relevant subgroups, highlighting its efficacy in improving quality of life, clinical, and PA pressure endpoints in chronic HF patients.


Asunto(s)
Insuficiencia Cardíaca , Arteria Pulmonar , Calidad de Vida , Humanos , Insuficiencia Cardíaca/terapia , Insuficiencia Cardíaca/fisiopatología , Femenino , Masculino , Anciano , Persona de Mediana Edad , Arteria Pulmonar/fisiopatología , Enfermedad Crónica , Volumen Sistólico/fisiología , Terapia de Resincronización Cardíaca/métodos , Desfibriladores Implantables
5.
Eur Radiol ; 2024 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-39014089

RESUMEN

BACKGROUND: Adding functional information by CT-derived fractional flow reserve (FFRct) to coronary CT angiography (CCTA) and assessing its temporal change may provide insight into the natural history and physiopathology of cardiac allograft vasculopathy (CAV) in heart transplantation (HTx) patients. We assessed FFRct changes as well as CAV progression over a 2-year period in HTx patients undergoing serial CT imaging. METHODS: HTx patients from Erasmus MC and Mount Sinai Hospital, who had consecutive CCTAs 2 years apart were evaluated. FFRct analysis was performed for both scans. FFRct values at the most distal point in the left anterior descending (LAD), left circumflex (LCX), and right coronary artery (RCA) were measured after precisely matching the anatomical locations in both analyses. Also, the number of anatomical coronary stenoses of > 30% was scored. RESULTS: In total, 106 patients (median age 57 [interquartile range 47-67] years, 67% male) at 9 [6-13] years after HTx at the time of the baseline CCTA were included. Median distal FFRct values significantly decreased from baseline to follow-up for the LAD from 0.85 [0.79-0.90] to 0.84 [0.76-0.90] (p = 0.001), LCX from 0.92 [0.88-0.96] to 0.91 [0.85-0.95] (p = 0.009), and RCA from 0.92 [0.86-0.95] to 0.90 [0.86-0.94] (p = 0.004). The number of focal anatomical stenoses of > 30% increased from a median of 1 [0-2] at baseline to 2 [0-3] at follow-up (p = 0.009). CONCLUSIONS: The distal coronary FFRct values in post-HTX patients in each of the three major coronary arteries decreased, and the number of focal coronary stenoses increased over a 2-year period. Temporal FFRct change rate may become an additional parameter in the follow-up of HTx patients, but more research is needed to elucidate its role. CLINICAL RELEVANCE STATEMENT: CT-derived fractional flow reserve (FFRct) is important post-heart transplant because of additional information on coronary CT angiography for cardiac allograft vasculopathy (CAV) detection. The decrease and degree of reduction in distal FFRct value may indicate progression in anatomic CAV burden. KEY POINTS: CT-derived fractional flow reserve (FFRct) is important for monitoring cardiac allograft vasculopathy (CAV) in heart transplant patients. Over time, transplant patients showed a decrease in distal FFRct and an increase in coronary stenoses. Temporal changes in FFRct could be crucial for transplant follow-up, aiding in CAV detection.

6.
Eur Heart J ; 44(31): 2911-2926, 2023 08 14.
Artículo en Inglés | MEDLINE | ID: mdl-37216272

RESUMEN

AIMS: Telemonitoring modalities in heart failure (HF) have been proposed as being essential for future organization and transition of HF care, however, efficacy has not been proven. A comprehensive meta-analysis of studies on home telemonitoring systems (hTMS) in HF and the effect on clinical outcomes are provided. METHODS AND RESULTS: A systematic literature search was performed in four bibliographic databases, including randomized trials and observational studies that were published during January 1996-July 2022. A random-effects meta-analysis was carried out comparing hTMS with standard of care. All-cause mortality, first HF hospitalization, and total HF hospitalizations were evaluated as study endpoints. Sixty-five non-invasive hTMS studies and 27 invasive hTMS studies enrolled 36 549 HF patients, with a mean follow-up of 11.5 months. In patients using hTMS compared with standard of care, a significant 16% reduction in all-cause mortality was observed [pooled odds ratio (OR): 0.84, 95% confidence interval (CI): 0.77-0.93, I2: 24%], as well as a significant 19% reduction in first HF hospitalization (OR: 0.81, 95% CI 0.74-0.88, I2: 22%) and a 15% reduction in total HF hospitalizations (pooled incidence rate ratio: 0.85, 95% CI 0.76-0.96, I2: 70%). CONCLUSION: These results are an advocacy for the use of hTMS in HF patients to reduce all-cause mortality and HF-related hospitalizations. Still, the methods of hTMS remain diverse, so future research should strive to standardize modes of effective hTMS.


Asunto(s)
Insuficiencia Cardíaca , Humanos , Insuficiencia Cardíaca/terapia , Hospitalización
7.
Sensors (Basel) ; 24(12)2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38931740

RESUMEN

With remarkable advancements in the development of connected and autonomous vehicles (CAVs), the integration of teleoperation has become crucial for improving safety and operational efficiency. However, teleoperation faces substantial challenges, with network latency being a critical factor influencing its performance. This survey paper explores the impact of network latency along with state-of-the-art mitigation/compensation approaches. It examines cascading effects on teleoperation communication links (i.e., uplink and downlink) and how delays in data transmission affect the real-time perception and decision-making of operators. By elucidating the challenges and available mitigation strategies, the paper offers valuable insights for researchers, engineers, and practitioners working towards the seamless integration of teleoperation in the evolving landscape of CAVs.

8.
Clin Infect Dis ; 76(3): e172-e178, 2023 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-35869843

RESUMEN

BACKGROUND: Illness after infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is less severe compared with previous variants. Data on the disease burden in immunocompromised patients are lacking. We investigated the clinical characteristics and outcomes of immunocompromised patients with coronavirus disease 2019 (COVID-19) caused by Omicron. METHODS: Organ transplant recipients, patients on anti-CD20 therapy, and allogenic hematopoietic stem cell transplantation recipients infected with the Omicron variant were included. Characteristics of consenting patients were collected and patients were contacted regularly until symptom resolution. To identify possible risk factors for hospitalization, a univariate logistic analysis was performed. RESULTS: 114 consecutive immunocompromised patients were enrolled. Eighty-nine percent had previously received 3 mRNA vaccinations. While only 1 patient died, 23 (20%) were hospitalized for a median of 11 days. A low SARS-CoV-2 immunoglobulin G (IgG) antibody response (<300 BAU [binding antibody units]/mL) at diagnosis, being older, being a lung transplant recipient, having more comorbidities, and having a higher frailty score were associated with hospital admission (all P < .01). At the end of follow-up, 25% had still not fully recovered. Of the 23 hospitalized patients, 70% had a negative and 92% had a low IgG (<300 BAU/mL) antibody response at admission. Sotrovimab was administered to 17 of these patients, and 1 died. CONCLUSIONS: While the mortality in immunocompromised patients infected with Omicron was low, hospital admission was frequent and the duration of symptoms often prolonged. In addition to vaccination, other interventions are needed to limit the morbidity from COVID-19 in immunocompromised patients.


Asunto(s)
Antígenos de Grupos Sanguíneos , COVID-19 , Humanos , SARS-CoV-2 , Estudios Prospectivos , Anticuerpos Antivirales , Huésped Inmunocomprometido , Inmunoglobulina G
9.
Rev Cardiovasc Med ; 24(11): 313, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-39076441

RESUMEN

Background: Right ventricular failure (RVF) is a significant cause of morbidity and mortality in patients with a left ventricular assist device (LVAD). This study is aimed to investigate the influence of a pectus excavatum on early and late outcomes, specifically RVF, following LVAD implantation. Methods: A retrospective study was performed, that included patients with a HeartMate 3 LVAD at our tertiary referral center. The Haller index (HI) was calculated using computed tomography (CT) scan to evaluate the chest-wall dimensions. Results: In total, 80 patients (median age 57 years) were included. Two cohorts were identified: 28 patients (35%) with a normal chest wall (HI < 2.0) and 52 patients (65%) with pectus excavatum (HI 2.0-3.2), with a mean follow-up time of 28 months. Early ( ≤ 30 days) RVF and early acute kidney injury events did not differ between cohorts. Overall survival did not differ between cohorts with a hazard ratio (HR) of 0.47 (95% confidence interval (CI): 0.19-1.19, p = 0.113). Late ( > 30 days) recurrent readmission for RVF occurred more often in patients with pectus excavatum (p = 0.008). The onset of late RVF started around 18 months after implantation and increased thereafter in the overall study cohort. Conclusions: Pectus excavatum is observed frequently in patients with a LVAD implantation. These patients have an increased rate of readmissions and late RVF. Further investigation is required to explore the extent and severity of chest-wall abnormalities on the risk of RVF.

10.
Eur Radiol ; 33(1): 330-338, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-35986769

RESUMEN

OBJECTIVES: Increasing evidence suggests a role for epicardial fat in the development of coronary artery disease in the general population. Heart transplantation patients are at increased risk of developing a specific form of coronary artery disease, cardiac allograft vasculopathy (CAV), which has far-reaching consequences in terms of morbidity and mortality. Until now, the role of epicardial fat volume (EFV) in the development of CAV remains unknown. Hence, we investigated the relationship between EFV and CAV as well as the influence of donor/recipient sex on EFV. METHODS: Adult heart transplant patients who underwent coronary computed tomography angiography (CCTA) for CAV screening who were four or more years post-HT were included. Using the CT examinations, we quantified the EFV and the degree of CAV. Ordinal and linear regression models were used to assess the association of EFV with CAV. RESULTS: In total, 149 (median age 44.5 years, 36% women) patients were included. The median time between HT and the CT scan was 11.0 (7.3-16.1) years. CAV grade 0, 1, 2 and 3 were seen in 85 (57%), 32 (22%), 14 (9%), and 18 (12%) patients, respectively. The median EFV was 208.4 (128.9-276.0) mL. Larger EFV were related to higher degrees of CAV (median of 164.7 to 290.6 mL for CAV grade 0 and 3, respectively, OR 5.23 (2.47-11.06), p < 0.001). Male recipients had significantly more EFV than female recipients irrespective of the donor sex (232.7 mL vs. 147.2 mL respectively, p < 0.001). Determinants for EFV were recipient sex, number of rejections, donor age, time between HT and CT scan, recipient BMI, and diabetes mellitus. CONCLUSIONS: EFV was associated with higher degrees of CAV. The recipient sex influenced the EFV more than the donor sex. KEY POINTS: • Patients after heart transplantation have a high amount of epicardial fat while larger amounts of epicardial fat are related to higher grades of cardiac allograft vasculopathy. • Determinants of higher epicardial fat volume included recipient sex, number of rejections, donor age, time between HT and CT scan, recipient BMI, and diabetes mellitus. • Longitudinal studies are needed to further disentangle the role of epicardial fat in the development and progression of cardiac allograft vasculopathy. Demonstration of four patients (from CAV grade 0 to CAV grade 3) in whom epicardial fat volume was determined. In red, the voxels identified as epicardial fat.


Asunto(s)
Enfermedad de la Arteria Coronaria , Cardiopatías , Trasplante de Corazón , Adulto , Humanos , Femenino , Masculino , Enfermedad de la Arteria Coronaria/diagnóstico por imagen , Enfermedad de la Arteria Coronaria/etiología , Pericardio/diagnóstico por imagen , Trasplante de Corazón/efectos adversos , Cardiopatías/etiología , Aloinjertos , Angiografía Coronaria , Factores de Riesgo
11.
Curr Oncol Rep ; 25(7): 753-763, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-37079251

RESUMEN

PURPOSE OF REVIEW: Immune checkpoint inhibitors (ICIs) have improved the field of cancer, especially in patients with advanced malignancies. Nevertheless, cardiovascular immune-related adverse events (irAEs) with high mortality and morbidity have been observed, including myocarditis, pericarditis, and vasculitis. To date, only a few clinical risk factors have been described and are currently being investigated. RECENT FINDINGS: In this review, we address the four most prevailing risk factors for cardiovascular irAEs. ICI combination therapy is a predominant risk factor for developing ICI-mediated myocarditis. Additionally, ICI combined with other anti-cancer treatments (e.g., tyrosine kinase inhibitors, radiation, chemotherapy) seems to increase the risk of developing cardiovascular irAEs. Other risk factors include female sex, pre-existing cardiovascular disease, and specific tumors, on which we will further elaborate in this review. An a priori risk strategy to determine who is at risk to develop these cardiovascular irAEs is needed. Insights into the impact of risk factors are therefore warranted to help clinicians improve care and disease management in these patients.


Asunto(s)
Antineoplásicos Inmunológicos , Sistema Cardiovascular , Miocarditis , Neoplasias , Humanos , Femenino , Inhibidores de Puntos de Control Inmunológico/efectos adversos , Miocarditis/inducido químicamente , Antineoplásicos Inmunológicos/efectos adversos , Factores de Riesgo
12.
Cardiovasc Drugs Ther ; 37(6): 1243-1248, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-36227441

RESUMEN

BACKGROUND: The presence of atrial fibrillation (AF) in heart failure (HF) patients with reduced ejection fraction is common and associated with an increased risk of stroke, hospitalization and mortality. Recent research findings indicate that a reduction in nicotinamide adenine dinucleotide (NAD+) levels results in mitochondrial dysfunction, DNA damage and consequently cardiomyocyte impairment in experimental and clinical HF and AF. The HF-AF ENERGY trial aims to investigate the cardioprotective effects of the NAD+ precursor nicotinamide riboside (NR) treatment in ischemic heart disease patients diagnosed with AF. STUDY DESIGN: The HF-AF ENERGY trial is a prospective intervention study. The study consists of a (retrospective) 4 months observation period and a 4 months intervention period. The cardioprotective effect of NR on AF burden is investigated by remote monitoring software of implantable cardiac defibrillators (ICDs), which enables continuous atrial rhythm monitoring detection. Cardiac dimension and function are examined by echocardiography. Laboratory blood analysis is performed to determine mitochondrial function markers and energy metabolism. All the study parameters are assessed at two fixed time points (pre- and post-treatment). Pre- and post-treatment outcomes are compared to determine the effects of NR treatment on AF burden, mitochondrial function markers and energy metabolism. CONCLUSION: The HF-AF ENERGY trial investigates the cardioprotective effects of NR on AF burden and whether NR normalizes blood-based mitochondrial function markers and energy metabolites of the NAD metabolome in ischemic heart disease patients diagnosed with AF. The study outcomes elucidate whether NAD+ metabolism can be used as a future therapy for HF patients with AF.


Asunto(s)
Fibrilación Atrial , Insuficiencia Cardíaca , Isquemia Miocárdica , Humanos , Fibrilación Atrial/diagnóstico , Fibrilación Atrial/tratamiento farmacológico , Fibrilación Atrial/complicaciones , NAD , Estudios Prospectivos , Estudios Retrospectivos , Volumen Sistólico , Insuficiencia Cardíaca/diagnóstico , Insuficiencia Cardíaca/tratamiento farmacológico , Isquemia Miocárdica/complicaciones
13.
Artículo en Inglés | MEDLINE | ID: mdl-36780068

RESUMEN

PURPOSE: Multiple randomized controlled trials have presented SGLT2 inhibitors (SGLT2i) as novel pharmacological therapy for patients with heart failure, resulting in reductions in hospitalization for heart failure and mortality. Given the absence of SGLT2 receptors in the heart, mechanisms of direct cardioprotective effects of SGLT2i are complex and remain to be investigated. In this study, we evaluated the direct biomechanical effects of SGLT2i empagliflozin on isolated myocardium from end-stage heart failure patients. METHODS: Ventricular tissue biopsies obtained from 7 patients undergoing heart transplantation or ventricular assist device implantation surgery were cut into 27 living myocardial slices (LMS) and mounted in custom-made cultivation chambers with mechanical preload and electrical stimulation, resulting in cardiac contractions. These 300 µm thick LMS were subjected to 10 µM empagliflozin and with continuous recording of biomechanical parameters. RESULTS: Empagliflozin did not affect the maximum contraction force of the slices, however, increased total contraction duration by 13% (p = 0.002) which was determined by prolonged time to peak and time to relaxation (p = 0.009 and p = 0.003, respectively). CONCLUSION: The addition of empagliflozin to LMS from end-stage heart failure patients cultured in a biomimetic system improves contraction and relaxation kinetics by increasing total contraction duration without diminishing maximum force production. Therefore, we present convincing evidence that SGLT2i can directly act on the myocardium in absence of systemic influences from other organ systems.

14.
Neth Heart J ; 31(2): 68-75, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-35838916

RESUMEN

BACKGROUND: Since 1998, there has been a national programme for paediatric heart transplantations (HT) in the Netherlands. In this study, we investigated waiting list mortality, survival post-HT, the incidence of common complications, and the patients' functional status during follow-up. METHODS: All children listed for HT from 1998 until October 2020 were included. Follow-up lasted until 1 January 2021. Data were collected from the patient charts. Survival, post-operative complications as well as the functional status (Karnofsky/Lansky scale) at the end of follow-up were measured. RESULTS: In total, 87 patients were listed for HT, of whom 19 (22%) died while on the waiting list. Four patients were removed from the waiting list and 64 (74%) underwent transplantation. Median recipient age at HT was 12.0 (IQR 7.2-14.4) years old; 55% were female. One-, 5­, and 10-year survival post-HT was 97%, 95%, and 88%, respectively. Common transplant-related complications were rejections (50%), Epstein-Barr virus infections (31%), cytomegalovirus infections (25%), post-transplant lymphoproliferative disease (13%), and cardiac allograft vasculopathy (13%). The median functional score (Karnofsky/Lansky scale) was 100 (IQR 90-100). CONCLUSION: Children who undergo HT have an excellent survival rate up to 10 years post-HT. Even though complications post-HT are common, the functional status of most patients is excellent. Waiting list mortality is high, demonstrating that donor availability for this vulnerable patient group remains a major limitation for further improvement of outcome.

15.
Extremes (Boston) ; 26(3): 573-594, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37581203

RESUMEN

Confounding variables are a recurrent challenge for causal discovery and inference. In many situations, complex causal mechanisms only manifest themselves in extreme events, or take simpler forms in the extremes. Stimulated by data on extreme river flows and precipitation, we introduce a new causal discovery methodology for heavy-tailed variables that allows the effect of a known potential confounder to be almost entirely removed when the variables have comparable tails, and also decreases it sufficiently to enable correct causal inference when the confounder has a heavier tail. We also introduce a new parametric estimator for the existing causal tail coefficient and a permutation test. Simulations show that the methods work well and the ideas are applied to the motivating dataset. Supplementary Information: The online version contains supplementary material available at 10.1007/s10687-022-00456-4.

16.
BMC Bioinformatics ; 23(1): 499, 2022 Nov 19.
Artículo en Inglés | MEDLINE | ID: mdl-36402957

RESUMEN

BACKGROUND: Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. RESULTS: In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. CONCLUSIONS: SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases.


Asunto(s)
Polimorfismo de Nucleótido Simple , Programas Informáticos , Mapeo Cromosómico , Marcadores Genéticos , Genotipo
17.
Proc Biol Sci ; 289(1985): 20221589, 2022 10 26.
Artículo en Inglés | MEDLINE | ID: mdl-36285501

RESUMEN

It is generally believed that marsupials are more primitive than placentals mammals and mainly solitary living, representing the ancestral form of social organization of all mammals. However, field studies have observed pair and group-living in marsupial species, but no comparative study about their social evolution was ever done. Here, we describe the results of primary literature research on marsupial social organization which indicates that most species can live in pairs or groups and many show intra-specific variation in social organization. Using Bayesian phylogenetic mixed-effects models with a weak phylogenetic signal of 0.18, we found that solitary living was the most likely ancestral form (35% posterior probability), but had high uncertainty, and the combined probability of a partly sociable marsupial ancestor (65%) should not be overlooked. For Australian marsupials, group-living species were less likely to be found in tropical rainforest, and species with a variable social organization were associated with low and unpredictable precipitation representing deserts. Our results suggest that modern marsupials are more sociable than previously believed and that there is no strong support that their ancestral state was strictly solitary living, such that the assumption of a solitary ancestral state of all mammals may also need reconsideration.


Asunto(s)
Marsupiales , Animales , Filogenia , Evolución Biológica , Teorema de Bayes , Australia , Mamíferos
18.
Eur Radiol ; 32(3): 1843-1852, 2022 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-34523009

RESUMEN

OBJECTIVES: Invasively measured fractional flow reserve (FFR) is associated with outcome in heart transplant (HTx) patients. Coronary computed tomography angiography (CCTA)-derived FFR (FFRct) provides additional functional information from anatomical CT images. We describe the first use of FFRct in HTx patients. METHODS: HTx patients underwent CCTA with FFRct to screen for cardiac allograft vasculopathy. FFRct was measured distal to each coronary stenosis > 30% and FFRct ≤ 0.8 indicated hemodynamically significant stenosis. FFRct was also measured at the most distal location of each vessel. Overall distal FFRct was calculated as the mean of the distal values in the left, right, and circumflex coronary artery in each patient. RESULTS: Seventy-three patients (age 56 (42-65) years, 63% males) at 11 (8-16) years after HTx were included. Eighteen (25%) patients had a focal hemodynamically significant stenosis (stenosis > 30% with FFRct ≤ 0.8). In the 55 patients without a hemodynamically significant focal FFRct stenosis (FFRct > 0.80), the distal left anterior descending artery FFRct was < 0.90 in 74% of the patients and 10 (18%) patients had ≥ 1 coronary artery with a distal FFRct ≤ 0.8, including 1 with a distal FFRct ≤ 0.8 in all coronaries. Overall distal FFRct in patients without focal stenosis was 0.88 (0.86-0.91), 0.87 (0.86-0.90), and 0.88 (0.86-0.91) (median with 25th-75th percentile) at 5-9, 10-14, or ≥ 15 years post-transplantation, respectively (p = 0.93). CONCLUSIONS: FFRct performed on CCTA scans of HTx patients demonstrated that 25% of patients had a focal coronary stenosis with FFRct ≤ 0.8. Even without a focal stenosis, FFRct values are often abnormal in HTx patients. KEY POINTS: • This is the first report describing the use of FFRct in in heart transplant patients. • FFRct identifies patients after heart transplantation with hemodynamically significant coronary stenosis. • Even without a focal stenosis, FFRct values are often abnormal in heart transplant patients.


Asunto(s)
Enfermedad de la Arteria Coronaria , Estenosis Coronaria , Reserva del Flujo Fraccional Miocárdico , Trasplante de Corazón , Angiografía por Tomografía Computarizada , Angiografía Coronaria , Estenosis Coronaria/diagnóstico por imagen , Vasos Coronarios/diagnóstico por imagen , Femenino , Estudios de Seguimiento , Humanos , Masculino , Persona de Mediana Edad , Valor Predictivo de las Pruebas , Índice de Severidad de la Enfermedad , Tomografía Computarizada por Rayos X
19.
Transpl Int ; 35: 10113, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35516977

RESUMEN

Post-transplant diabetes mellitus (PTDM) is a frequent complication post-heart transplantation (HT), however long-term prevalence studies are missing. The aim of this study was to determine the prevalence and determinants of PTDM as well as prediabetes long-term post-HT using oral glucose tolerance tests (OGTT). Also, the additional value of OGTT compared to fasting glucose and glycated hemoglobin (HbA1c) was investigated. All patients > 1 year post-HT seen at the outpatient clinic between August 2018 and April 2021 were screened with an OGTT. Patients with known diabetes, an active infection/rejection/malignancy or patients unwilling or unable to undergo OGTT were excluded. In total, 263 patients were screened, 108 were excluded. The included 155 patients had a median age of 54.3 [42.2-64.3] years, and 63 (41%) were female. Median time since HT was 8.5 [4.8-14.5] years. Overall, 51 (33%) had a normal range, 85 (55%) had a prediabetes range and 19 (12%) had a PTDM range test. OGTT identified prediabetes and PTDM in more patients (18% and 50%, respectively), than fasting glucose levels and HbA1c. Age at HT (OR 1.03 (1.00-1.06), p = 0.044) was a significant determinant of an abnormal OGTT. Prediabetes as well as PTDM are frequently seen long-term post-HT. OGTT is the preferred screening method.


Asunto(s)
Diabetes Mellitus , Intolerancia a la Glucosa , Trasplante de Corazón , Estado Prediabético , Adulto , Glucemia , Diabetes Mellitus/etiología , Femenino , Intolerancia a la Glucosa/diagnóstico , Intolerancia a la Glucosa/epidemiología , Intolerancia a la Glucosa/etiología , Prueba de Tolerancia a la Glucosa , Hemoglobina Glucada/análisis , Trasplante de Corazón/efectos adversos , Humanos , Masculino , Persona de Mediana Edad , Estado Prediabético/diagnóstico , Estado Prediabético/epidemiología , Estado Prediabético/etiología
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