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1.
Pediatr Res ; 2024 May 22.
Article in English | MEDLINE | ID: mdl-38778228

ABSTRACT

BACKGROUND AND AIM: Caffeine is routinely used for the prophylaxis of prematurity-related apnoeas. We aimed to evaluate the effect of caffeine maintenance on cardiovascular and cerebrovascular haemodynamics using a non-invasive multimodal monitoring in preterm infants during the transitional period. METHODS: Infants <32 weeks' gestational age (GA) were enrolled in this observational prospective study. The following parameters were recorded before and after the administration of caffeine citrate 5 mg/kg using near-infrared spectroscopy, pulse oximetry and electrical velocimetry: heart rate, cardiac output, stroke volume, cardiac contractility, systemic vascular resistance (SVR), perfusion index, peripheral and cerebral oxygenation, cerebral fractional oxygen extraction, correlation index between cerebral oxygenation and heart rate (TOHRx, marker of cerebrovascular reactivity). Multilevel mixed-effects linear models were used to assess the impact of caffeine and of relevant clinical covariates on each parameter. RESULTS: Seventy-seven infants (mean GA 29.3 ± 2.5 weeks, mean birthweight 1148 ± 353 g) were included. Caffeine administration was associated with increased SVR (B = 0.623, p = 0.004) and more negative TOHRx values (B = -0.036, p = 0.022), which suggest improved cerebrovascular reactivity. CONCLUSIONS: Caffeine administration at maintenance dosage during postnatal transition is associated with increased systemic vascular tone and improved cerebrovascular reactivity. A possible role for caffeine-mediated inhibition of adenosine receptors may be hypothesized. IMPACT: This study provides a thorough and comprehensive overview of multiple cerebrovascular and cardiovascular parameters, monitored non-invasively by combining near-infrared spectroscopy, electrical velocimetry and pulse oximetry, before and after the administration of caffeine at maintenance dosage in preterm infants during postnatal transition. Caffeine was associated with an improvement in cerebrovascular reactivity and with a slight but significant increase in systemic vascular resistance, with no additional effects on other cardiovascular and cerebrovascular parameters. Our results support the safety of caffeine treatment even during a phase at risk for haemodynamic instability such as postnatal transition and suggest potential beneficial effects on cerebral haemodynamics.

2.
Eur J Neurol ; 31(1): e16070, 2024 01.
Article in English | MEDLINE | ID: mdl-37724995

ABSTRACT

BACKGROUND AND PURPOSE: Hereditary transthyretin amyloidosis (ATTRv) is a life-threatening disease caused by mutations in the gene encoding transthyretin (TTR). The recent therapeutic advances have underlined the importance of easily accessible, objective biomarkers of both disease onset and progression. Preliminary evidence suggests a potential role in this respect for neurofilament light chain (NfL). In this study, the aim was to determine serum NfL (sNfL) levels in a late-onset ATTRv population and evaluate whether it might represent a reliable biomarker of disease onset (i.e., 'conversion' from the asymptomatic status to symptomatic disease in TTR mutation carriers). METHODS: In all, 111 individuals harbouring a pathogenic TTR variant (61 symptomatic ATTRv patients and 50 presymptomatic carriers) were consecutively enrolled. Fifty healthy volunteers were included as the control group. Ella™ apparatus was used to assess sNfL levels. RESULTS: Serum NfL levels were increased in ATTRv patients compared to both presymptomatic carriers and healthy controls, whilst not differing between carriers and healthy controls. An sNfL cut-off of 37.10 pg/mL could discriminate between asymptomatic and symptomatic individuals with high diagnostic accuracy (area under the curve 0.958; p < 0.001), sensitivity (81.4%) and specificity (100%). CONCLUSIONS: Serum NfL seems to be a promising biomarker of peripheral nerve involvement in ATTRv amyloidosis and might become a reliable, objective measure to detect the transition from the presymptomatic stage to the onset of symptomatic disease. Further longitudinal studies are needed to confirm such a role and determine whether it could equally represent a biomarker of disease progression and response to therapy.


Subject(s)
Amyloid Neuropathies, Familial , Intermediate Filaments , Humans , Amyloid Neuropathies, Familial/diagnosis , Amyloid Neuropathies, Familial/genetics , Amyloid Neuropathies, Familial/pathology , Longitudinal Studies , Biomarkers
3.
Neurol Sci ; 45(4): 1675-1684, 2024 Apr.
Article in English | MEDLINE | ID: mdl-37938457

ABSTRACT

BACKGROUND: Hereditary transthyretin (ATTRv) amyloidosis is a heterogeneous, progressive, multisystemic disease with a life-threatening course if left untreated. Given the current availability of effective therapies, close follow-up of presymptomatic TTR mutation carriers is essential to recognize disease onset at the earliest sign. In addition to routine techniques, in recent years several novel tools have been proposed, although a consensus on their use has not been reached yet. In this paper, we aimed to evaluate possible markers of neuropathic disease onset intended to discriminate clinically asymptomatic carriers from early symptomatic patients, thus allowing timely treatment initiation. METHODS: Thirty-eight presymptomatic carriers were enrolled. Clinical and electrophysiological findings at first evaluation and follow-up were collected. All carriers underwent an extensive clinical and instrumental evaluation according to the standard clinical practice. One or more non-routine investigations, whose use in this field is not yet validated (henceforth "unconventional"), were additionally assessed in a subgroup of individuals. RESULTS: Based on the exclusive use of routine investigations, it was possible to define disease onset in 4/38 carriers during the follow-up. Employing additionally one or more "unconventional" tests, abnormal findings, indicative of a possible "conversion" to symptomatic disease, were detected in further 12 cases. More than half of our study cohort showed findings suggestive of small nerve fiber (SF) involvement at either invasive or non-invasive tests. CONCLUSIONS: A close, multidisciplinary monitoring of presymptomatic TTR mutation carriers is fundamental, and diagnostic workup should include both routine and "unconventional" tests. Assessment of SF involvement is important also in non-endemic countries.


Subject(s)
Amyloid Neuropathies, Familial , Humans , Amyloid Neuropathies, Familial/diagnosis , Amyloid Neuropathies, Familial/genetics , Amyloid Neuropathies, Familial/therapy , Prealbumin/genetics , Early Diagnosis , Mutation/genetics
4.
Int J Mol Sci ; 25(2)2024 Jan 19.
Article in English | MEDLINE | ID: mdl-38279256

ABSTRACT

Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is an immune-mediated disorder affecting the peripheral nervous system. Despite the established diagnostic criteria, monitoring disease activity and treatment remains challenging. To address this limitation, we investigated serum neurofilament light chain (sNfL) and serum free light chains (sFLCs) as potential biomarkers. A total of 32 CIDP patients undergoing immunoglobulin therapy and 32 healthy controls enrolled in the present study, and agreed to have their blood plasma sNfL and sFLCs analyzed, while CIDP severity was assessed through the modified Rankin Scale (mRS) and the Overall Neuropathy Limitations Scale (ONLS). In line with the immunoglobulin treatment aimed at limiting neuronal damage administered to the majority of patients, sNfL levels did not exhibit significant differences between the two groups. However, CIDP patients showed significantly elevated sFLC and sFLC ratios, while the marker levels did not correlate with the clinical scores. The study confirms the potential of sFLCs as a sensitive biomarker of inflammatory processes in CIDP. Additionally, the present study results regarding neurofilaments strengthen the role of sNfL in monitoring CIDP treatments, confirming the effectiveness of immunoglobulin therapy. Overall, our results demonstrate how combining these markers can lead to better patient characterization for improved treatment.


Subject(s)
Polyradiculoneuropathy, Chronic Inflammatory Demyelinating , Humans , Polyradiculoneuropathy, Chronic Inflammatory Demyelinating/diagnosis , Polyradiculoneuropathy, Chronic Inflammatory Demyelinating/drug therapy , Intermediate Filaments , Immunoglobulin Light Chains , Biomarkers
5.
Eur J Pediatr ; 182(9): 4247-4251, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37458816

ABSTRACT

This prospective observational study aimed to evaluate whether lung fluids, assessed by lung ultrasonography and transthoracic electrical bioimpedance (TEB), may be influenced by the presence of a haemodynamically significant patent ductus arteriosus (hsPDA) in very preterm infants during the transitional period. Infants < 32 weeks of gestational age (GA) admitted to the neonatal intensive care units of IRCCS AOU Bologna and Niguarda Metropolitan Hospital of Milan (Italy) underwent a daily assessment of a lung ultrasound score (LUS) and of a TEB-derived index of thoracic fluid contents (TFC) during the first 72 h after birth. Echocardiographic scans were simultaneously performed to evaluate the concomitant ductal status (hsPDA vs. restrictive or closed duct). The correlation between LUS, TFC, and the ductal status was tested using generalized estimating equations. Forty-six infants (median GA: 29 [interquartile range, IQR: 27-31] weeks; median birth weight: 1099 [IQR: 880-1406] g) were included. At each daily evaluation, the presence of a hsPDA was associated with significantly higher LUS and TFC compared with a restrictive or closed ductus (p < 0.01 for all comparisons). These results were confirmed significant even after adjustment for GA and for the ongoing modality of respiratory support. Conclusion: Even during the first 72 h of life, the presence of a hsPDA determines a significant increase in pulmonary fluids which can be non-invasively detected and monitored over time using lung ultrasonography and TEB. What is Known: • Lung ultrasonography provides a non-invasive assessment of lung fluids and is widely used in neonatal settings. • In preterm infants, the persistence of a haemodynamically significant patent ductus arteriosus (hsPDA) over the first weeks can negatively affect pulmonary outcomes. What is New: • The presence of aan hsPDA is associated with increased lung fluids since early postnatal phases. • Lung ultrasonography and transthoracic electrical bioimpedance can effectively monitor lung fluid clearance in preterm infants with a hsPDA during the transitional period, with potential clinical implications.

6.
Learn Mem ; 29(9): 321-331, 2022 09.
Article in English | MEDLINE | ID: mdl-36206387

ABSTRACT

Age, genetics, and chromosomal sex have been identified as critical risk factors for late-onset Alzheimer's disease (LOAD). The predominant genetic risk factor for LOAD is the apolipoprotein E ε4 allele (APOE4), and the prevalence of LOAD is higher in females. However, the translational validity of APOE4 mouse models for AD-related cognitive impairment remains to be fully determined. The present study investigated the role of both sex and genotype on learning and memory in aged, humanized APOE knock-in mice. Aged (23.27 mo ± 1.21 mo; 39 male/37 female) APOE3/3, APOE3/4, and APOE4/4 mice performed a novel object recognition (NOR) assay. Task-related metrics were analyzed using two-way sex by genotype ANOVAs. Sex differences were more prominent relative to APOE genotype. Prior to NOR, female mice exhibited thigmotaxic center zone avoidance during the open field task relative to males, regardless of genotype. Within object familiarization and NOR tasks, females had greater object interaction and locomotion. Interestingly, only APOE4/4 females on average recognized the novel object. These results suggest that APOE4, although strongly related to LOAD pathogenesis, does not drive cognitive decline in the absence of other risk factors even in very aged mice. Chromosomal sex is a key driver of behavioral phenotypes and thus is a critical variable for translatability of interventions designed to preserve learning and memory in animal models of LOAD. Last, there was a very high degree of variability in behavioral performance across APOE genotypes. A cluster analysis of the behavioral data revealed a low-activity and a high-activity cluster. APOE4 carriers were overrepresented in the low-activity cluster, while male:female distributions did not differ. Collectively, the behavioral data indicate that chromosomal sex has the greatest impact on behavioral phenotype, and APOE4 carrier status may confer greater risk for cognitive decline in some animals.


Subject(s)
Alzheimer Disease , Apolipoprotein E4 , Alzheimer Disease/genetics , Animals , Apolipoprotein E3/genetics , Apolipoprotein E4/genetics , Disease Models, Animal , Exploratory Behavior , Female , Genotype , Male , Mice , Mice, Transgenic
7.
J Vasc Surg ; 75(1): 223-228, 2022 01.
Article in English | MEDLINE | ID: mdl-34478810

ABSTRACT

OBJECTIVE: We sought to determine whether extracranial carotid atherosclerotic disease (ECAD) is associated with increased key neurodegenerative pathology such as neurofibrillary tangle (NFT), beta-amyloid plaque, or cerebral amyloid angiopathy (CAA) accumulation, findings associated with Alzheimer's disease (AD) and other dementias. METHODS: Our prospective, longitudinal, clinicopathologic study, the AZSAND (Arizona study of aging and neurodegenerative disorders) and Brain and Body Donation Program, recorded the presence or absence of clinically diagnosed ECAD and performed semiquantitative density estimates of NFT, beta-amyloid plaque, and CAA at death. After adjusting for potential confounding factors determined by logistic regression analysis, histopathology density scores were evaluated in individuals with ECAD (n = 66) and those without ECAD (n = 125). RESULTS: We found that the presence of ECAD was associated with a 21% greater NFT burden at death compared with no ECAD (P = .02). Anatomically, an increased NFT burden was seen throughout the brain regions evaluated but was significant in the temporal lobe (P < .05) and entorhinal cortex (P = .02). In addition, we found that subjects who had undergone carotid endarterectomy (CEA), the surgical treatment of ECAD (n = 32), had decreased NFT densities compared with those with ECAD who had not undergone CEA (n = 66; P = .04). In contrast to NFT, ECAD was not associated with beta-amyloid plaques or CAA density. CONCLUSIONS: These findings indicate that ECAD is associated with the NFT burden in the temporal lobe and entorhinal cortex, which has clinical significance for AD and non-AD dementias and cognitive dysfunction. Further understanding of whether ECAD increases the risk of neurodegenerative brain changes is highly relevant because ECAD is a treatable disease that has not, otherwise, been evaluated for nor specifically treated as a dementia risk factor.


Subject(s)
Alzheimer Disease/epidemiology , Carotid Artery Diseases/epidemiology , Cerebral Amyloid Angiopathy/epidemiology , Cognitive Dysfunction/epidemiology , Neurofibrillary Tangles/pathology , Plaque, Amyloid/epidemiology , Aged , Aged, 80 and over , Alzheimer Disease/diagnosis , Alzheimer Disease/pathology , CA1 Region, Hippocampal/pathology , Cerebral Amyloid Angiopathy/diagnosis , Cerebral Amyloid Angiopathy/pathology , Cognitive Dysfunction/diagnosis , Cognitive Dysfunction/pathology , Entorhinal Cortex/pathology , Humans , Longitudinal Studies , Male , Middle Aged , Plaque, Amyloid/diagnosis , Plaque, Amyloid/pathology , Prospective Studies , Risk Assessment/statistics & numerical data , Risk Factors
8.
Pediatr Res ; 92(1): 135-141, 2022 07.
Article in English | MEDLINE | ID: mdl-35513715

ABSTRACT

BACKGROUND: Preterm infants are at enhanced risk of brain injury due to altered cerebral haemodynamics during postnatal transition. This observational study aimed to assess the clinical determinants of transitional cerebrovascular reactivity and its association with intraventricular haemorrhage (IVH). METHODS: Preterm infants <32 weeks underwent continuous monitoring of cerebral oxygenation and heart rate over the first 72 h after birth. Serial cranial and cardiac ultrasound assessments were performed to evaluate the ductal status and to diagnose IVH onset. The moving correlation coefficient between cerebral oxygenation and heart rate (TOHRx) was calculated. Linear mixed-effect models were used to analyse the impact of relevant clinical variables on TOHRx. The association between TOHRx and IVH development was also assessed. RESULTS: Seventy-seven infants were included. A haemodynamically significant patent ductus arteriosus (hsPDA) (ß = 0.044, 95% CI: 0.007-0.081) and ongoing dopamine treatment (ß = 0.096, 95% CI: 0.032-0.159) were associated with increasing TOHRx, indicating impaired cerebrovascular reactivity. A significant association between TOHRx, mean arterial blood pressure (ß = -0.004, 95% CI: -0.007, -0.001) and CRIB-II score (ß = 0.007, 95% CI: 0.001-0.015) was also observed. TOHRx was significantly higher in infants developing high-grade IVH compared to those without IVH. CONCLUSIONS: Dopamine treatment, low blood pressure, hsPDA and high CRIB-II are associated with impaired cerebrovascular reactivity during postnatal transition, with potential implications on IVH development. IMPACT: The correlation coefficient between cerebral oxygenation and heart rate (TOHRx) provides a non-invasive estimation of cerebrovascular reactivity, whose failure has a potential pathogenic role in the development of IVH in preterm infants. This study shows that cerebrovascular reactivity during the transitional period improves over time and is affected by specific clinical and therapeutic factors, whose knowledge could support the development of individualized neuroprotective strategies in at-risk preterm infants. The evidence of increased TOHRx in infants developing high-grade compared to low-grade or no IVH during the transitional period further supports the role of impaired cerebrovascular reactivity in IVH pathophysiology.


Subject(s)
Ductus Arteriosus, Patent , Infant, Premature, Diseases , Cerebral Hemorrhage , Cerebrovascular Circulation/physiology , Dopamine , Female , Fetal Growth Retardation , Humans , Infant , Infant, Newborn , Infant, Premature
9.
Pediatr Res ; 91(7): 1715-1722, 2022 06.
Article in English | MEDLINE | ID: mdl-34897282

ABSTRACT

BACKGROUND: Following preterm birth, the immature kidney is exposed to several harmful conditions, with an increased risk of renal impairment. We aimed to assess urinary biomarkers of renal function in very preterm infants during early nephrotoxic treatments. METHODS: Infants ≤32 weeks' gestation and ≤1500 g were enrolled in this observational prospective study. Urine samples were collected on day 1(T1), 2-4(T2), 5-7(T3), 8-10(T4), 11-13(T5). The following urinary biomarkers were determined: osteopontin (uOPN), epidermal growth factor (uEGF), neutrophil gelatinase-associated lipocalin (uNGAL), cystatin C (uCysC). The infants were grouped according to their exposure to amikacin or ibuprofen during the study period and a between-group comparison of urinary biomarkers at each time point was performed. RESULTS: Thirty-six infants were included. Urinary CysC, uOPN, and uNGAL rose significantly during ibuprofen or amikacin treatment, while no difference was observed for uEGF. After adjustment for possible influencing factors, amikacin administration was associated with higher uCysC at T1 (p = 0.007) and T2 (p = 0.016), whereas ibuprofen increased uOPN (p = 0.001) and uNGAL concentration (p = 0.009) at T3. CONCLUSION: Nephrotoxic therapies induce molecule-specific change patterns of renal function biomarkers in treated preterm infants. Serial assessments of these biomarkers may aid to identify neonates at risk of renal impairment and to develop tailored therapeutic approaches. IMPACT: Despite the wide use of nephrotoxic therapies in neonatal settings, little is known on their effect on renal function biomarkers in preterm infants. This study describes molecule-specific change patterns of urinary biomarkers during ibuprofen and amikacin administration, suggesting underlying pathophysiological effects on renal function. Given their low analytical costs and non-invasive collection, the urinary biomarkers investigated in this study represent a promising strategy for serial monitoring of renal function in at-risk neonates and may aid the early detection of renal function impairment at different kidney levels during nephrotoxic treatments.


Subject(s)
Acute Kidney Injury , Infant, Premature, Diseases , Premature Birth , Acute Kidney Injury/chemically induced , Acute Kidney Injury/diagnosis , Acute Kidney Injury/urine , Amikacin/adverse effects , Biomarkers/urine , Female , Humans , Ibuprofen/adverse effects , Infant , Infant, Newborn , Infant, Premature/urine , Kidney/physiology , Lipocalin-2/urine , Pharmaceutical Preparations , Prospective Studies
10.
Int J Mol Sci ; 23(24)2022 Dec 17.
Article in English | MEDLINE | ID: mdl-36555770

ABSTRACT

Hereditary transthyretin amyloidosis is the most common form of hereditary amyloidosis, with an autosomal dominant inheritance and a variable penetrance. ATTRv amyloidosis can present as a progressive, axonal sensory autonomic and motor neuropathy or as an infiltrative cardiomyopathy. The definition of biomarkers for the early diagnosis of ATTRv is particularly important in the current era of emerging treatments. In this sense, metabolomics could be an instrument able to provide metabolic profiles with their related metabolic pathways, and we would propose them as possible fluid biomarkers. The aim of this study is to identify altered metabolites (free fatty acids and amino acids) in subjects with a confirmed pathogenic TTR variant. Out of the studied total free fatty acids and amino acids, the serum values of palmitic acid are significantly lower in the ATTRv patients compared to the recruited healthy subjects. The metabolic remodeling identified in this neurogenetic disorder could be the manifestation of pathophysiological processes of the disease, such as mitochondrial dysfunction and neuroinflammation, and contribute to explaining some of its clinical manifestations.


Subject(s)
Amyloid Neuropathies, Familial , Amyloidosis, Familial , Humans , Pilot Projects , Fatty Acids, Nonesterified , Amyloid Neuropathies, Familial/pathology , Prealbumin/genetics
11.
Brief Bioinform ; 20(3): 789-805, 2019 05 21.
Article in English | MEDLINE | ID: mdl-29272327

ABSTRACT

The development of computational methods capable of analyzing -omics data at the individual level is critical for the success of precision medicine. Although unprecedented opportunities now exist to gather data on an individual's -omics profile ('personalome'), interpreting and extracting meaningful information from single-subject -omics remain underdeveloped, particularly for quantitative non-sequence measurements, including complete transcriptome or proteome expression and metabolite abundance. Conventional bioinformatics approaches have largely been designed for making population-level inferences about 'average' disease processes; thus, they may not adequately capture and describe individual variability. Novel approaches intended to exploit a variety of -omics data are required for identifying individualized signals for meaningful interpretation. In this review-intended for biomedical researchers, computational biologists and bioinformaticians-we survey emerging computational and translational informatics methods capable of constructing a single subject's 'personalome' for predicting clinical outcomes or therapeutic responses, with an emphasis on methods that provide interpretable readouts. Key points: (i) the single-subject analytics of the transcriptome shows the greatest development to date and, (ii) the methods were all validated in simulations, cross-validations or independent retrospective data sets. This survey uncovers a growing field that offers numerous opportunities for the development of novel validation methods and opens the door for future studies focusing on the interpretation of comprehensive 'personalomes' through the integration of multiple -omics, providing valuable insights into individual patient outcomes and treatments.


Subject(s)
Precision Medicine , Transcriptome , Humans
12.
Eur J Pediatr ; 180(9): 3047-3051, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33839913

ABSTRACT

Perfluoroalkyl substances (PFASs) are environmental contaminants that have been shown to exert toxic effects, which are dependent upon concentration, in animals and humans. No specific data on the exposure of preterm infants to PFASs are available. We aimed to quantify the potential exposure of preterm infants to PFASs through human milk (HM), to be compared to the exposure data recently reported for infants by EFSA. The amount of PFASs in ten preterm (PHM) and ten donor HM (DHM) samples was evaluated, and the expected daily intake (EDI) at full enteral feeding was calculated. This EDI was compared to the mean and the 95th centile dietary exposure ranges at the lower bound for infants issued by EFSA. The calculated median EDI for total PFASs was 20.72 ng/kg/day (range 10.72-107.84) for PHM and 17.92 ng/kg/day (range 6.4-28.96) for DHM, which were both higher than mean exposure ranges reported for infants (2.4-12.2 ng/kg/day). The calculated EDI for DHM was far more similar to the 95th centile (4.5-27.9 ng/kg/day) dietary exposure ranges. For PHM samples, higher EDI values were obtained, with 4 out of 10 samples exceeding the upper limit of the 95th centile range.Conclusion: The exposure of preterm infants to PFASs through HM feeding might exceed reference values reported for older and healthier infants. Given the immunological and developmental vulnerability of preterm infants, the risks related to their exposure to PFASs should be further investigated, also focusing on how maternal exposure and subsequent transfer through HM feeding can be reduced. What is Known: • Perfluoroalkyl substances (PFASs) are environmental contaminants that have been shown to exert toxic effects, which are dependent upon concentration, in animals and humans. The EFSA has recently issued reference values for PFASs exposure for different age groups. • Infants might be exposed to PFASs prenatally, as these substances can cross the placenta, and postnatally, through breastfeeding. No specific data about exposure of preterm infants through human milk (HM) feeding are currently available. What is New: • The exposure of preterm infants to PFASs through HM feeding might exceed reference values reported for older and healthier infants. • Given the immunological and developmental vulnerability of preterm infants, the risks related to their exposure to PFASs deserve further investigation. As HM represents the optimal feeding for preterm infants, it will be fundamental to focus on how maternal exposure and subsequent transfer through HM feeding can be reduced.


Subject(s)
Fluorocarbons , Animals , Enteral Nutrition , Female , Fluorocarbons/analysis , Fluorocarbons/toxicity , Humans , Infant , Infant, Newborn , Infant, Premature , Milk, Human/chemistry , Placenta/chemistry , Pregnancy
13.
BMC Bioinformatics ; 21(1): 219, 2020 May 29.
Article in English | MEDLINE | ID: mdl-32471360

ABSTRACT

BACKGROUND: Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among transcription factors (TFs) and their target genes, with a method able to handle both the high number of interacting variables and the noise in the available heterogeneous experimental sources of information. RESULTS: In this work, we propose a data fusion approach that exploits the integration of complementary omics-data as prior knowledge within a Bayesian framework, in order to learn and model large-scale transcriptional networks. We develop a hybrid structure-learning algorithm able to jointly combine TFs ChIP-Sequencing data and gene expression compendia to reconstruct TRNs in a genome-wide perspective. Applying our method to high-throughput data, we verified its ability to deal with the complexity of a genomic TRN, providing a snapshot of the synergistic TFs regulatory activity. Given the noisy nature of data-driven prior knowledge, which potentially contains incorrect information, we also tested the method's robustness to false priors on a benchmark dataset, comparing the proposed approach to other regulatory network reconstruction algorithms. We demonstrated the effectiveness of our framework by evaluating structural commonalities of our learned genomic network with other existing networks inferred by different DNA binding information-based methods. CONCLUSIONS: This Bayesian omics-data fusion based methodology allows to gain a genome-wide picture of the transcriptional interplay, helping to unravel key hierarchical transcriptional interactions, which could be subsequently investigated, and it represents a promising learning approach suitable for multi-layered genomic data integration, given its robustness to noisy sources and its tailored framework for handling high dimensional data.


Subject(s)
Gene Regulatory Networks , Algorithms , Bayes Theorem , Chromatin Immunoprecipitation Sequencing , Genomics/methods , Transcription Factors/metabolism
14.
Bioinformatics ; 35(6): 923-929, 2019 03 15.
Article in English | MEDLINE | ID: mdl-30169576

ABSTRACT

MOTIVATION: Protein cleavage is an important cellular event, involved in a myriad of processes, from apoptosis to immune response. Bioinformatics provides in silico tools, such as machine learning-based models, to guide the discovery of targets for the proteases responsible for protein cleavage. State-of-the-art models have a scope limited to specific protease families (such as Caspases), and do not explicitly include biological or medical knowledge (such as the hierarchical protein domain similarity or gene-gene interactions). To fill this gap, we present a novel approach for protease target prediction based on data integration. RESULTS: By representing protease-protein target information in the form of relational matrices, we design a model (i) that is general and not limited to a single protease family, and (b) leverages on the available knowledge, managing extremely sparse data from heterogeneous data sources, including primary sequence, pathways, domains and interactions. When compared with other algorithms on test data, our approach provides a better performance even for models specifically focusing on a single protease family. AVAILABILITY AND IMPLEMENTATION: https://gitlab.com/smarini/MaDDA/ (Matlab code and utilized data.). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Algorithms , Software , Computer Simulation , Machine Learning , Peptide Hydrolases
15.
J Pediatr ; 221: 32-38.e2, 2020 06.
Article in English | MEDLINE | ID: mdl-32446489

ABSTRACT

OBJECTIVE: To investigate the features of cardiorespiratory events in infants born preterm during the transitional period, and to evaluate whether different neonatal characteristics may correlate with event type, duration, and severity. STUDY DESIGN: Infants with gestational age (GA) <32 weeks and/or birth weight <1500 g were enrolled in this observational prospective study. Heart rate (HR) and peripheral oxygen saturation (SpO2) were recorded continuously over the first 72 hours. Cardiorespiratory events of ≥10 seconds were clustered into isolated desaturation (SpO2 <85%), isolated bradycardia (HR <100 bpm or <70% of baseline), or combined desaturation/bradycardia and classified as mild, moderate, or severe. The daily incidences of isolated desaturation, isolated bradycardia, and combined desaturation and bradycardia were analyzed. The effects of relevant clinical variables on cardiorespiratory event type and severity were assessed using generalized estimating equations. RESULTS: Among the 1050 events analyzed, isolated desaturations were the most frequent (n = 625) and isolated bradycardias the least common (n = 171). The number of cardiorespiratory events increased significantly from day 1 to day 2 (P = .028). One in 5 events had severe characteristics; event severity was highest for combined desaturation and bradycardia (P < .001). Compared with other event types, the incidence of combined desaturation and bradycardia was inversely correlated with GA (P = .029) and was higher with the use of continuous positive airway pressure (P = .002). The presence of a hemodynamically significant patent ductus arteriosus was associated with the occurrence of isolated desaturations (P = .001) and with a longer duration of cardiorespiratory events (P = .003). CONCLUSIONS: Cardiorespiratory events during transition exhibit distinct types, duration, and severity. Neonatal characteristics are associated with the clinical features of these events, indicating that a tailored clinical approach may reduce the hypoxic burden in preterm infants aged 0-72 hours.


Subject(s)
Bradycardia/epidemiology , Hypoxia/epidemiology , Female , Humans , Infant, Newborn , Infant, Premature , Male , Prospective Studies , Time Factors
16.
J Pediatr Gastroenterol Nutr ; 70(4): 508-512, 2020 04.
Article in English | MEDLINE | ID: mdl-31880664

ABSTRACT

OBJECTIVES: Human milk (HM) feeding leads to improved outcome for preterm infants. When mother's milk is unavailable, pasteurized donor HM (DHM) is the recommended alternative over formula. The Holder pasteurization (HoP) method is universally performed in HM banks; however, it is known to impair several functional HM components. The aim of this study was to compare the efficacy of HoP with 2 innovative processing methods (high-temperature short-time [HTST] pasteurization and high-pressure processing [HPP]) in preserving some bioactive HM protein components. METHODS: HM samples from donors of the Bologna HM bank were collected and divided into 4 subsamples: 1 was kept raw, and each of the others was processed using a different technique (HoP, HTST, and HPP at 600 MPa for 3 minutes). Total protein content, secretory immunoglobulin A (sIgA), and lactoferrin contents were compared. RESULTS: Both HM lactoferrin and sIgA content were negatively affected, but to a different extent, by each method: sIgA was preserved by HTST, with only HPP leading to a significant reduction (-38.8%); lactoferrin content was strongly reduced by HoP (-87.5%) and HTST (-83.5%), and preserved by HPP. Variations in protein profile were seen for all processing methods, being more relevant for HoP, followed by HTST and, finally, by HPP. All the 3 methods lowered the untreated HM microbial counts to undetectable levels, in accordance with national guidelines. CONCLUSIONS: Both HTST and HPP better preserved the original HM protein profile, compared to HoP. They, however, affected differently some bioactive HM components involved in immune response and antibacterial activity.


Subject(s)
Milk Banks , Pasteurization , Humans , Infant , Infant, Newborn , Infant, Premature , Milk Proteins/analysis , Milk, Human/chemistry
17.
J Pediatr Gastroenterol Nutr ; 69(4): 493-497, 2019 10.
Article in English | MEDLINE | ID: mdl-31211764

ABSTRACT

Because of its possible effect on mesenteric blood flow, the presence of a hemodynamically significant patent ductus arteriosus (PDA) is often of concern for the introduction of enteral feeds in preterm neonates. Near-infrared spectroscopy allows a continuous monitoring of splanchnic oxygenation (SrSO2) and may provide useful hemodynamic information. This observational study evaluated SrSO2 patterns in response to first feed administration in 50 preterm infants <32 weeks' gestation with different ductal status. According to their echocardiographic characteristics, the enrolled infants were divided into the following groups: pulsatile PDA with hemodynamically significant features, restrictive PDA, and no evidence of PDA. The presence of PDA, either with restrictive or hemodynamically significant characteristics, does not significantly affect SrSO2 response to enteral feeding introduction and is not associated with increased rates of gut complications. This finding may provide encouraging evidence in support of early enteral nutrition in very preterm infants with PDA.


Subject(s)
Ductus Arteriosus, Patent/physiopathology , Enteral Nutrition , Infant, Premature , Oxygen/metabolism , Cohort Studies , Female , Hemodynamics , Humans , Infant, Newborn , Male , Pilot Projects , Prospective Studies , Spectroscopy, Near-Infrared
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