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1.
Clin Transl Sci ; 17(3): e13740, 2024 03.
Artigo em Inglês | MEDLINE | ID: mdl-38411371

RESUMO

Fibromyalgia patients vary in clinical phenotype and treatment can be challenging. The pathophysiology of fibromyalgia is incompletely understood but appears to involve metabolic changes at rest or in response to stress. We enrolled 54 fibromyalgia patients and 31 healthy controls to this prospective study. Symptoms were assessed using the Fibromyalgia Impact Questionnaire (FIQ) and blood samples were collected for metabolomics analysis at baseline and after an oral glucose tolerance test and a cardiopulmonary exercise test. We identified key symptoms of fibromyalgia and related them to changes in metabolic pathways with supervised and unsupervised machine learning methods. Algorithms trained with the FIQ information assigned the fibromyalgia diagnosis in new data with balanced accuracy of 88% while fatigue alone already provided the diagnosis with 86% accuracy. Supervised analyses reduced the metabolomic information from 77 to 13 key markers. With these metabolites, fibromyalgia could be identified in new cases with 79% accuracy. In addition, 5-hydroxyindole-3-acetic acid and glutamine levels correlated with the severity of fatigue. Patients differed from controls at baseline in tyrosine and purine pathways, and in the pyrimidine pathway after the stress challenges. Several key markers are involved in glutaminergic neurotransmission. This data-driven analysis highlights fatigue as a key symptom of fibromyalgia. Fibromyalgia is associated with metabolic changes which also reflect the degree of fatigue. Responses to metabolic and physical stresses result in a metabolic pattern that allows discrimination of fibromyalgia patients from controls and narrows the focus on key pathophysiological processes in fibromyalgia as treatment targets.


Assuntos
Fibromialgia , Humanos , Fibromialgia/diagnóstico , Tirosina , Estudos Prospectivos , Fadiga/diagnóstico , Fadiga/etiologia , Aprendizado de Máquina , Purinas , Pirimidinas
2.
Chem Senses ; 492024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-38401152

RESUMO

Clinical assessment of an individual's sense of smell has gained prominence, but its resource-intensive nature necessitates the exploration of self-administered methods. In this study, a cohort of 68 patients with olfactory loss and 55 controls were assessed using a recently introduced olfactory test. This test involves sorting 2 odorants (eugenol and phenylethyl alcohol) in 5 dilutions according to odor intensity, with an average application time of 3.5 min. The sorting task score, calculated as the mean of Kendall's Tau between the assigned and true dilution orders and normalized to [0,1], identified a cutoff for anosmia at a score ≤ 0.7. This cutoff, which marks the 90th percentile of scores obtained with randomly ordered dilutions, had a balanced accuracy of 89% (78% to 97%) for detecting anosmia, comparable to traditional odor threshold assessments. Retest evaluations suggested a score difference of ±0.15 as a cutoff for clinically significant changes in olfactory function. In conclusion, the olfactory sorting test represents a simple, self-administered approach to the detection of anosmia or preserved olfactory function. With balanced accuracy similar to existing brief olfactory tests, this method offers a practical and user-friendly alternative for screening anosmia, addressing the need for resource-efficient assessments in clinical settings.


Assuntos
Odorantes , Transtornos do Olfato , Humanos , Transtornos do Olfato/diagnóstico , Anosmia , Reprodutibilidade dos Testes , Limiar Sensorial , Olfato
3.
Chem Senses ; 492024 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-38213039

RESUMO

Loss of olfactory function is a typical acute coronavirus disease 2019 (COVID-19) symptom, at least in early variants of SARS-CoV2. The time that has elapsed since the emergence of COVID-19 now allows for assessing the long-term prognosis of its olfactory impact. Participants (n = 722) of whom n = 464 reported having had COVID-19 dating back with a mode of 174 days were approached in a museum as a relatively unbiased environment. Olfactory function was diagnosed by assessing odor threshold and odor identification performance. Subjects also rated their actual olfactory function on an 11-point numerical scale [0,…10]. Neither the frequency of olfactory diagnostic categories nor olfactory test scores showed any COVID-19-related effects. Olfactory diagnostic categories (anosmia, hyposmia, or normosmia) were similarly distributed among former patients and controls (0.86%, 18.97%, and 80.17% for former patients and 1.17%, 17.51%, and 81.32% for controls). Former COVID-19 patients, however, showed differences in their subjective perception of their own olfactory function. The impact of this effect was substantial enough that supervised machine learning algorithms detected past COVID-19 infections in new subjects, based on reduced self-awareness of olfactory performance and parosmia, while the diagnosed olfactory function did not contribute any relevant information in this context. Based on diagnosed olfactory function, results suggest a positive prognosis for COVID-19-related olfactory loss in the long term. Traces of former infection are found in self-perceptions of olfaction, highlighting the importance of investigating the long-term effects of COVID-19 using reliable and validated diagnostic measures in olfactory testing.


Assuntos
COVID-19 , Transtornos do Olfato , Humanos , SARS-CoV-2 , RNA Viral , Olfato , Transtornos do Olfato/diagnóstico , Anosmia/diagnóstico , Anosmia/etiologia , Aprendizado de Máquina Supervisionado
4.
Expert Rev Clin Pharmacol ; 17(1): 79-91, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38165148

RESUMO

BACKGROUND: Clinical pharmacology research has always involved computational analysis. With the abundance of drug-related data available, the integration of artificial intelligence (AI) and machine learning (ML) methods has emerged as a promising way to enhance clinical pharmacology research. METHODS: Based on an accepted definition of clinical pharmacology as a field of research dealing with all aspects of drug-human interactions, the analysis included publications from institutes specializing in clinical pharmacology. Research topics and the most used machine learning methods in clinical pharmacology were retrieved from the PubMed database and summarized. RESULTS: ML was identified in 674 publications attributed to clinical pharmacology research, with a significant increase in publication activity over the last decade. Notable research topics addressed by ML/AI included Covid-19-related clinical pharmacology research, clinical neuropharmacology, drug safety and risk assessment, clinical pharmacology related to cancer research, and antimicrobial and antiviral research unrelated to Covid-19. In terms of ML methods, neural networks, random forests, and support vector machines were frequently mentioned in the abstracts of the retrieved papers. CONCLUSIONS: ML, and AI in general, is increasingly being used in various research areas within clinical pharmacology. This report presents specific examples of applications and highlights the most used ML methods.


Assuntos
COVID-19 , Farmacologia Clínica , Humanos , Inteligência Artificial , Aprendizado de Máquina
5.
Sci Rep ; 13(1): 22710, 2023 12 19.
Artigo em Inglês | MEDLINE | ID: mdl-38123604

RESUMO

Psoriatic arthritis (PsA) is a chronic inflammatory systemic disease whose activity is often assessed using the Disease Activity Score 28 (DAS28-CRP). The present study was designed to investigate the significance of individual components within the score for PsA activity. A cohort of 80 PsA patients (44 women and 36 men, aged 56.3 ± 12 years) with a range of disease activity from remission to moderate was analyzed using unsupervised and supervised methods applied to the DAS28-CRP components. Machine learning-based permutation importance identified tenderness in the metacarpophalangeal joint of the right index finger as the most informative item of the DAS28-CRP for PsA activity staging. This symptom alone allowed a machine learned (random forests) classifier to identify PsA remission with 67% balanced accuracy in new cases. Projection of the DAS28-CRP data onto an emergent self-organizing map of artificial neurons identified outliers, which following augmentation of group sizes by emergent self-organizing maps based generative artificial intelligence (AI) could be defined as subgroups particularly characterized by either tenderness or swelling of specific joints. AI-assisted re-evaluation of the DAS28-CRP for PsA has narrowed the score items to a most relevant symptom, and generative AI has been useful for identifying and characterizing small subgroups of patients whose symptom patterns differ from the majority. These findings represent an important step toward precision medicine that can address outliers.


Assuntos
Artrite Psoriásica , Masculino , Humanos , Feminino , Artrite Psoriásica/diagnóstico , Artrite Psoriásica/tratamento farmacológico , Inteligência Artificial , Algoritmos , Articulação Metacarpofalângica , Aprendizado de Máquina
6.
Sci Rep ; 13(1): 17923, 2023 10 20.
Artigo em Inglês | MEDLINE | ID: mdl-37864001

RESUMO

Random walks describe stochastic processes characterized by a sequence of unpredictable changes in a random variable with no correlation to past changes. This report describes the random walk component of a clinical sensory test of olfactory performance. The precise definition of this stochastic process allows the establishment of precise diagnostic cut-offs for the identification of olfactory loss. Within the Sniffin`Sticks olfactory test battery, odor discrimination (D) and odor identification (I) are assessed by four- and three-alternative forced-choice designs, respectively. Meanwhile, the odor threshold (T) test integrates a three-alternative forced-choice paradigm within a staircase paradigm with seven turning points. We explored this paradigm through computer simulations and provided a formal description. The odor threshold assessment test consists of two sequential components, the first of which sets the starting point for the second. Both parts can be characterized as biased random walks with significantly different probabilities of moving to higher (11%) or lower (89%) values. The initial odor concentration step for the first phase of the test and the length of the subsequent random walk in the second phase significantly affect the probability of randomly achieving high test scores. Changing the odor concentration from where the starting point determination for the second test part begins has raised the current cut-off for anosmia, represented as T + D + I < 16, from the 87th quantile of random test scores to the 97th quantile. Analogous findings are likely applicable to other sensory tests that use the staircase paradigm characterized as random walk.


Assuntos
Transtornos do Olfato , Olfato , Humanos , Limiar Sensorial , Odorantes , Simulação por Computador , Fontes de Energia Elétrica , Transtornos do Olfato/diagnóstico
7.
Sci Rep ; 13(1): 7332, 2023 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-37147321

RESUMO

Sex differences in pain perception have been extensively studied, but precision medicine applications such as sex-specific pain pharmacology have barely progressed beyond proof-of-concept. A data set of pain thresholds to mechanical (blunt and punctate pressure) and thermal (heat and cold) stimuli applied to non-sensitized and sensitized (capsaicin, menthol) forearm skin of 69 male and 56 female healthy volunteers was analyzed for data structures contingent with the prior sex structure using unsupervised and supervised approaches. A working hypothesis that the relevance of sex differences could be approached via reversibility of the association, i.e., sex should be identifiable from pain thresholds, was verified with trained machine learning algorithms that could infer a person's sex in a 20% validation sample not seen to the algorithms during training, with balanced accuracy of up to 79%. This was only possible with thresholds for mechanical stimuli, but not for thermal stimuli or sensitization responses, which were not sufficient to train an algorithm that could assign sex better than by guessing or when trained with nonsense (permuted) information. This enabled the translation to the molecular level of nociceptive targets that convert mechanical but not thermal information into signals interpreted as pain, which could eventually be used for pharmacological precision medicine approaches to pain. By exploiting a key feature of machine learning, which allows for the recognition of data structures and the reduction of information to the minimum relevant, experimental human pain data could be characterized in a way that incorporates "non" logic that could be translated directly to the molecular pharmacological level, pointing toward sex-specific precision medicine for pain.


Assuntos
Hiperalgesia , Limiar da Dor , Humanos , Feminino , Masculino , Limiar da Dor/fisiologia , Medição da Dor , Dor , Capsaicina/farmacologia , Temperatura Alta , Aprendizado de Máquina
8.
Eur J Pain ; 27(7): 787-793, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37222242

Assuntos
Dor , Humanos
9.
Sci Rep ; 13(1): 5470, 2023 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-37016033

RESUMO

Selecting the k best features is a common task in machine learning. Typically, a few features have high importance, but many have low importance (right-skewed distribution). This report proposes a numerically precise method to address this skewed feature importance distribution in order to reduce a feature set to the informative minimum of items. Computed ABC analysis (cABC) is an item categorization method that aims to identify the most important items by partitioning a set of non-negative numerical items into subsets "A", "B", and "C" such that subset "A" contains the "few important" items based on specific properties of ABC curves defined by their relationship to Lorenz curves. In its recursive form, the cABC analysis can be applied again to subset "A". A generic image dataset and three biomedical datasets (lipidomics and two genomics datasets) with a large number of variables were used to perform the experiments. The experimental results show that the recursive cABC analysis limits the dimensions of the data projection to a minimum where the relevant information is still preserved and directs the feature selection in machine learning to the most important class-relevant information, including filtering feature sets for nonsense variables. Feature sets were reduced to 10% or less of the original variables and still provided accurate classification in data not used for feature selection. cABC analysis, in its recursive variant, provides a computationally precise means of reducing information to a minimum. The minimum is the result of a computation of the number of k most relevant items, rather than a decision to select the k best items from a list. In addition, there are precise criteria for stopping the reduction process. The reduction to the most important features can improve the human understanding of the properties of the data set. The cABC method is implemented in the Python package "cABCanalysis" available at https://pypi.org/project/cABCanalysis/ .

10.
Pharmacol Ther ; 241: 108312, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36423714

RESUMO

Morphine prescribed for analgesia has caused drug-related deaths at an estimated incidence of 0.3% to 4%. Morphine has pharmacological properties that make it particularly difficult to assess the causality of morphine administration with a patient's death, such as its slow transfer between plasma and central nervous sites of action and the existence of the active metabolite morphine-6-glucuronide with opioid agonistic effects, Furthermore, there is no well-defined toxic dose or plasma/blood concentration for morphine. Dosing is often adjusted for adequate pain relief. Here, we summarize reported deaths associated with morphine therapy, including associated morphine exposure and modulating patient factors such as pharmacogenetics, concomitant medications, or comorbidities. In addition, we systematically analyzed published numerical information on the stability of concentrations of morphine and its relevant metabolites in biological samples collected postmortem. A medicolegal case is presented in which the causality of morphine administration with death was in dispute and pharmacokinetic modeling was applied to infer the administered dose. The results of this analytical review suggest that (i) inference from postmortem blood concentrations to the morphine dose administered has low validity and (ii) causality between a patient's death and the morphine dose administered remains a highly context-dependent and collaborative assessment among experts from different medical specialties.


Assuntos
Analgésicos Opioides , Morfina , Humanos , Morfina/efeitos adversos , Analgésicos Opioides/farmacologia , Ciência de Dados , Derivados da Morfina/farmacocinética , Derivados da Morfina/uso terapêutico , Dor/tratamento farmacológico
11.
Int J Mol Sci ; 23(22)2022 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-36430580

RESUMO

Bayesian inference is ubiquitous in science and widely used in biomedical research such as cell sorting or "omics" approaches, as well as in machine learning (ML), artificial neural networks, and "big data" applications. However, the calculation is not robust in regions of low evidence. In cases where one group has a lower mean but a higher variance than another group, new cases with larger values are implausibly assigned to the group with typically smaller values. An approach for a robust extension of Bayesian inference is proposed that proceeds in two main steps starting from the Bayesian posterior probabilities. First, cases with low evidence are labeled as "uncertain" class membership. The boundary for low probabilities of class assignment (threshold ε) is calculated using a computed ABC analysis as a data-based technique for item categorization. This leaves a number of cases with uncertain classification (p < ε). Second, cases with uncertain class membership are relabeled based on the distance to neighboring classified cases based on Voronoi cells. The approach is demonstrated on biomedical data typically analyzed with Bayesian statistics, such as flow cytometric data sets or biomarkers used in medical diagnostics, where it increased the class assignment accuracy by 1−10% depending on the data set. The proposed extension of the Bayesian inference of class membership can be used to obtain robust and plausible class assignments even for data at the extremes of the distribution and/or for which evidence is weak.


Assuntos
Big Data , Pesquisa Biomédica , Teorema de Bayes , Probabilidade , Incerteza
12.
Pain Rep ; 7(6): e1044, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36348668

RESUMO

The collection of increasing amounts of data in health care has become relevant for pain therapy and research. This poses problems for analyses with classical approaches, which is why artificial intelligence (AI) and machine learning (ML) methods are being included into pain research. The current literature on AI and ML in the context of pain research was automatically searched and manually curated. Common machine learning methods and pain settings covered were evaluated. Further focus was on the origin of the publication and technical details, such as the included sample sizes of the studies analyzed with ML. Machine learning was identified in 475 publications from 18 countries, with 79% of the studies published since 2019. Most addressed pain conditions included low back pain, musculoskeletal disorders, osteoarthritis, neuropathic pain, and inflammatory pain. Most used ML algorithms included random forests and support vector machines; however, deep learning was used when medical images were involved in the diagnosis of painful conditions. Cohort sizes ranged from 11 to 2,164,872, with a mode at n = 100; however, deep learning required larger data sets often only available from medical images. Artificial intelligence and ML, in particular, are increasingly being applied to pain-related data. This report presents application examples and highlights advantages and limitations, such as the ability to process complex data, sometimes, but not always, at the cost of big data requirements or black-box decisions.

13.
J Clin Med ; 11(14)2022 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-35887775

RESUMO

BACKGROUND: The categorization of individuals as normosmic, hyposmic, or anosmic from test results of odor threshold, discrimination, and identification may provide a limited view of the sense of smell. The purpose of this study was to expand the clinical diagnostic repertoire by including additional tests. METHODS: A random cohort of n = 135 individuals (83 women and 52 men, aged 21 to 94 years) was tested for odor threshold, discrimination, and identification, plus a distance test, in which the odor of peanut butter is perceived, a sorting task of odor dilutions for phenylethyl alcohol and eugenol, a discrimination test for odorant enantiomers, a lateralization test with eucalyptol, a threshold assessment after 10 min of exposure to phenylethyl alcohol, and a questionnaire on the importance of olfaction. Unsupervised methods were used to detect structure in the olfaction-related data, followed by supervised feature selection methods from statistics and machine learning to identify relevant variables. RESULTS: The structure in the olfaction-related data divided the cohort into two distinct clusters with n = 80 and 55 subjects. Odor threshold, discrimination, and identification did not play a relevant role for cluster assignment, which, on the other hand, depended on performance in the two odor dilution sorting tasks, from which cluster assignment was possible with a median 100-fold cross-validated balanced accuracy of 77-88%. CONCLUSIONS: The addition of an odor sorting task with the two proposed odor dilutions to the odor test battery expands the phenotype of olfaction and fits seamlessly into the sensory focus of standard test batteries.

14.
BMC Bioinformatics ; 23(1): 233, 2022 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-35710346

RESUMO

BACKGROUND: Data transformations are commonly used in bioinformatics data processing in the context of data projection and clustering. The most used Euclidean metric is not scale invariant and therefore occasionally inappropriate for complex, e.g., multimodal distributed variables and may negatively affect the results of cluster analysis. Specifically, the squaring function in the definition of the Euclidean distance as the square root of the sum of squared differences between data points has the consequence that the value 1 implicitly defines a limit for distances within clusters versus distances between (inter-) clusters. METHODS: The Euclidean distances within a standard normal distribution (N(0,1)) follow a N(0,[Formula: see text]) distribution. The EDO-transformation of a variable X is proposed as [Formula: see text] following modeling of the standard deviation s by a mixture of Gaussians and selecting the dominant modes via item categorization. The method was compared in artificial and biomedical datasets with clustering of untransformed data, z-transformed data, and the recently proposed pooled variable scaling. RESULTS: A simulation study and applications to known real data examples showed that the proposed EDO scaling method is generally useful. The clustering results in terms of cluster accuracy, adjusted Rand index and Dunn's index outperformed the classical alternatives. Finally, the EDO transformation was applied to cluster a high-dimensional genomic dataset consisting of gene expression data for multiple samples of breast cancer tissues, and the proposed approach gave better results than classical methods and was compared with pooled variable scaling. CONCLUSIONS: For multivariate procedures of data analysis, it is proposed to use the EDO transformation as a better alternative to the established z-standardization, especially for nontrivially distributed data. The "EDOtrans" R package is available at https://cran.r-project.org/package=EDOtrans .


Assuntos
Algoritmos , Biologia Computacional , Análise por Conglomerados , Genômica , Distribuição Normal
15.
Int J Mol Sci ; 23(9)2022 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-35563473

RESUMO

Recent scientific evidence suggests that chronic pain phenotypes are reflected in metabolomic changes. However, problems associated with chronic pain, such as sleep disorders or obesity, may complicate the metabolome pattern. Such a complex phenotype was investigated to identify common metabolomics markers at the interface of persistent pain, sleep, and obesity in 71 men and 122 women undergoing tertiary pain care. They were examined for patterns in d = 97 metabolomic markers that segregated patients with a relatively benign pain phenotype (low and little bothersome pain) from those with more severe clinical symptoms (high pain intensity, more bothersome pain, and co-occurring problems such as sleep disturbance). Two independent lines of data analysis were pursued. First, a data-driven supervised machine learning-based approach was used to identify the most informative metabolic markers for complex phenotype assignment. This pointed primarily at adenosine monophosphate (AMP), asparagine, deoxycytidine, glucuronic acid, and propionylcarnitine, and secondarily at cysteine and nicotinamide adenine dinucleotide (NAD) as informative for assigning patients to clinical pain phenotypes. After this, a hypothesis-driven analysis of metabolic pathways was performed, including sleep and obesity. In both the first and second line of analysis, three metabolic markers (NAD, AMP, and cysteine) were found to be relevant, including metabolic pathway analysis in obesity, associated with changes in amino acid metabolism, and sleep problems, associated with downregulated methionine metabolism. Taken together, present findings provide evidence that metabolomic changes associated with co-occurring problems may play a role in the development of severe pain. Co-occurring problems may influence each other at the metabolomic level. Because the methionine and glutathione metabolic pathways are physiologically linked, sleep problems appear to be associated with the first metabolic pathway, whereas obesity may be associated with the second.


Assuntos
Dor Crônica , Metaboloma , Monofosfato de Adenosina/metabolismo , Biomarcadores/metabolismo , Dor Crônica/genética , Dor Crônica/metabolismo , Cisteína/metabolismo , Feminino , Humanos , Aprendizado de Máquina , Metabolômica/métodos , Metionina/metabolismo , NAD/metabolismo , Obesidade/metabolismo , Fenótipo , Transtornos do Sono-Vigília
16.
Int J Mol Sci ; 23(7)2022 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-35408848

RESUMO

BACKGROUND: Persistent postsurgical neuropathic pain (PPSNP) can occur after intraoperative damage to somatosensory nerves, with a prevalence of 29-57% in breast cancer surgery. Proteomics is an active research field in neuropathic pain and the first results support its utility for establishing diagnoses or finding therapy strategies. METHODS: 57 women (30 non-PPSNP/27 PPSNP) who had experienced a surgeon-verified intercostobrachial nerve injury during breast cancer surgery, were examined for patterns in 74 serum proteomic markers that allowed discrimination between subgroups with or without PPSNP. Serum samples were obtained both before and after surgery. RESULTS: Unsupervised data analyses, including principal component analysis and self-organizing maps of artificial neurons, revealed patterns that supported a data structure consistent with pain-related subgroup (non-PPSPN vs. PPSNP) separation. Subsequent supervised machine learning-based analyses revealed 19 proteins (CD244, SIRT2, CCL28, CXCL9, CCL20, CCL3, IL.10RA, MCP.1, TRAIL, CCL25, IL10, uPA, CCL4, DNER, STAMPB, CCL23, CST5, CCL11, FGF.23) that were informative for subgroup separation. In cross-validated training and testing of six different machine-learned algorithms, subgroup assignment was significantly better than chance, whereas this was not possible when training the algorithms with randomly permuted data or with the protein markers not selected. In particular, sirtuin 2 emerged as a key protein, presenting both before and after breast cancer treatments in the PPSNP compared with the non-PPSNP subgroup. CONCLUSIONS: The identified proteins play important roles in immune processes such as cell migration, chemotaxis, and cytokine-signaling. They also have considerable overlap with currently known targets of approved or investigational drugs. Taken together, several lines of unsupervised and supervised analyses pointed to structures in serum proteomics data, obtained before and after breast cancer surgery, that relate to neuroinflammatory processes associated with the development of neuropathic pain after an intraoperative nerve lesion.


Assuntos
Neoplasias da Mama , Neuralgia , Traumatismos do Sistema Nervoso , Neoplasias da Mama/complicações , Neoplasias da Mama/cirurgia , Quimiocinas , Feminino , Humanos , Aprendizado de Máquina , Neuralgia/complicações , Dor Pós-Operatória/complicações , Proteômica , Sirtuína 2 , Traumatismos do Sistema Nervoso/complicações
17.
Mol Biol Cell ; 33(6): ar60, 2022 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-35171646

RESUMO

Internalin B-mediated activation of the membrane-bound receptor tyrosine kinase MET is accompanied by a change in receptor mobility. Conversely, it should be possible to infer from receptor mobility whether a cell has been treated with internalin B. Here, we propose a method based on hidden Markov modeling and explainable artificial intelligence that machine-learns the key differences in MET mobility between internalin B-treated and -untreated cells from single-particle tracking data. Our method assigns receptor mobility to three diffusion modes (immobile, slow, and fast). It discriminates between internalin B-treated and -untreated cells with a balanced accuracy of >99% and identifies three parameters that are most affected by internalin B treatment: a decrease in the mobility of slow molecules (1) and a depopulation of the fast mode (2) caused by an increased transition of fast molecules to the slow mode (3). Our approach is based entirely on free software and is readily applicable to the analysis of other membrane receptors.


Assuntos
Inteligência Artificial , Imagem Individual de Molécula , Ligantes , Aprendizado de Máquina , Proteínas Proto-Oncogênicas c-met/metabolismo
18.
J Clin Med ; 10(21)2021 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-34768493

RESUMO

Because it is associated with central nervous changes, and olfactory dysfunction has been reported with increased prevalence among persons with diabetes, this study addressed the question of whether the risk of developing diabetes in the next 10 years is reflected in olfactory symptoms. In a cross-sectional study, in 164 individuals seeking medical consulting for possible diabetes, olfactory function was evaluated using a standardized clinical test assessing olfactory threshold, odor discrimination, and odor identification. Metabolomics parameters were assessed via blood concentrations. The individual diabetes risk was quantified according to the validated German version of the "FINDRISK" diabetes risk score. Machine learning algorithms trained with metabolomics patterns predicted low or high diabetes risk with a balanced accuracy of 63-75%. Similarly, olfactory subtest results predicted the olfactory dysfunction category with a balanced accuracy of 85-94%, occasionally reaching 100%. However, olfactory subtest results failed to improve the prediction of diabetes risk based on metabolomics data, and metabolomics data did not improve the prediction of the olfactory dysfunction category based on olfactory subtest results. Results of the present study suggest that olfactory function is not a useful predictor of diabetes.

19.
CPT Pharmacometrics Syst Pharmacol ; 10(11): 1371-1381, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34598320

RESUMO

The evaluation of pharmacological data using machine learning requires high data quality. Therefore, data preprocessing, that is, cleaning analytical laboratory errors, replacing missing values or outliers, and transforming data adequately before actual data analysis, is crucial. Because current tools available for this purpose often require programming skills, preprocessing tools with graphical user interfaces that can be used interactively are needed. In collaboration between data scientists and experts in bioanalytical diagnostics, a graphical software package for data preprocessing called pguIMP is proposed, which contains a fixed sequence of preprocessing steps to enable reproducible interactive data preprocessing. As an R-based package, it also allows direct integration into this data science environment without requiring any programming knowledge. The implementation of contemporary data processing methods, including machine-learning-based imputation techniques, ensures the generation of corrected and cleaned bioanalytical data sets that preserve data structures such as clusters better than is possible with classical methods. This was evaluated on bioanalytical data sets from lipidomics and drug research using k-nearest-neighbors-based imputation followed by k-means clustering and density-based spatial clustering of applications with noise. The R package provides a Shiny-based web interface designed to be easy to use for non-data analysis experts. It is demonstrated that the spectrum of methods provided is suitable as a standard pipeline for preprocessing bioanalytical data in biomedical research domains. The R package pguIMP is freely available at the comprehensive R archive network (https://cran.r-project.org/web/packages/pguIMP/index.html).


Assuntos
Confiabilidade dos Dados , Software , Humanos
20.
J Clin Med ; 10(18)2021 Sep 18.
Artigo em Inglês | MEDLINE | ID: mdl-34575356

RESUMO

Chronic rhinosinusitis (CRS) is often treated by functional endoscopic paranasal sinus surgery, which improves endoscopic parameters and quality of life, while olfactory function was suggested as a further criterion of treatment success. In a prospective cohort study, 37 parameters from four categories were recorded from 60 men and 98 women before and four months after endoscopic sinus surgery, including endoscopic measures of nasal anatomy/pathology, assessments of olfactory function, quality of life, and socio-demographic or concomitant conditions. Parameters containing relevant information about changes associated with surgery were examined using unsupervised and supervised methods, including machine-learning techniques for feature selection. The analyzed cohort included 52 men and 38 women. Changes in the endoscopic Lildholdt score allowed separation of baseline from postoperative data with a cross-validated accuracy of 85%. Further relevant information included primary nasal symptoms from SNOT-20 assessments, and self-assessments of olfactory function. Overall improvement in these relevant parameters was observed in 95% of patients. A ranked list of criteria was developed as a proposal to assess the outcome of functional endoscopic sinus surgery in CRS patients with nasal polyposis. Three different facets were captured, including the Lildholdt score as an endoscopic measure and, in addition, disease-specific quality of life and subjectively perceived olfactory function.

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