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1.
Article in English | MEDLINE | ID: mdl-38679324

ABSTRACT

BACKGROUND: Patients with major depressive disorder (MDD) can present with altered brain structure and deficits in cognitive function similar to aging. Yet, the interaction between age-related brain changes and brain development in MDD remains understudied. In a cohort of adolescents and adults with and without MDD, we assessed brain aging differences and associations through a newly developed tool quantifying normative neurodevelopmental trajectories. METHODS: 304 MDD participants and 236 non-depressed controls were recruited and scanned from three studies under the Canadian Biomarker Integration Network for Depression. Volumetric data were used to generate brain centile scores, which were examined for: a) differences in MDD relative to controls; b) differences in individuals with versus without severe childhood maltreatment; and c) correlations with depressive symptom severity, neurocognitive assessment domains, or escitalopram treatment response. RESULTS: Brain centiles were significantly lower in the MDD group compared to controls. It was also significantly correlated with working memory in controls, but not the MDD group. No significant associations were observed in depression severity or antidepressant treatment response with brain centiles. Likewise, childhood maltreatment history did not significantly affect brain centiles. CONCLUSIONS: Consistent with prior work on machine learning models that predict "brain age", brain centile scores differed in people diagnosed with MDD, and MDD was associated with differential relationships between centile scores and working memory. The results support the notion of atypical development and aging in MDD, with implications on neurocognitive deficits associated with aging-related cognitive function.

2.
J Cheminform ; 16(1): 40, 2024 Apr 07.
Article in English | MEDLINE | ID: mdl-38582911

ABSTRACT

Poly ADP-ribose polymerase 1 (PARP1) is an attractive therapeutic target for cancer treatment. Machine-learning scoring functions constitute a promising approach to discovering novel PARP1 inhibitors. Cutting-edge PARP1-specific machine-learning scoring functions were investigated using semi-synthetic training data from docking activity-labelled molecules: known PARP1 inhibitors, hard-to-discriminate decoys property-matched to them with generative graph neural networks and confirmed inactives. We further made test sets harder by including only molecules dissimilar to those in the training set. Comprehensive analysis of these datasets using five supervised learning algorithms, and protein-ligand fingerprints extracted from docking poses and ligand only features revealed one highly predictive scoring function. This is the PARP1-specific support vector machine-based regressor, when employing PLEC fingerprints, which achieved a high Normalized Enrichment Factor at the top 1% on the hardest test set (NEF1% = 0.588, median of 10 repetitions), and was more predictive than any other investigated scoring function, especially the classical scoring function employed as baseline.

3.
Health Data Sci ; 4: 0108, 2024.
Article in English | MEDLINE | ID: mdl-38486621

ABSTRACT

Background: Gemcitabine is a first-line chemotherapy for pancreatic adenocarcinoma (PAAD), but many PAAD patients do not respond to gemcitabine-containing treatments. Being able to predict such nonresponders would hence permit the undelayed administration of more promising treatments while sparing gemcitabine life-threatening side effects for those patients. Unfortunately, the few predictors of PAAD patient response to this drug are weak, none of them exploiting yet the power of machine learning (ML). Methods: Here, we applied ML to predict the response of PAAD patients to gemcitabine from the molecular profiles of their tumors. More concretely, we collected diverse molecular profiles of PAAD patient tumors along with the corresponding clinical data (gemcitabine responses and clinical features) from the Genomic Data Commons resource. From systematically combining 8 tumor profiles with 16 classification algorithms, each of the resulting 128 ML models was evaluated by multiple 10-fold cross-validations. Results: Only 7 of these 128 models were predictive, which underlines the importance of carrying out such a large-scale analysis to avoid missing the most predictive models. These were here random forest using 4 selected mRNAs [0.44 Matthews correlation coefficient (MCC), 0.785 receiver operating characteristic-area under the curve (ROC-AUC)] and XGBoost combining 12 DNA methylation probes (0.32 MCC, 0.697 ROC-AUC). By contrast, the hENT1 marker obtained much worse random-level performance (practically 0 MCC, 0.5 ROC-AUC). Despite not being trained to predict prognosis (overall and progression-free survival), these ML models were also able to anticipate this patient outcome. Conclusions: We release these promising ML models so that they can be evaluated prospectively on other gemcitabine-treated PAAD patients.

4.
Oncogene ; 43(16): 1223-1230, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38413794

ABSTRACT

CIC::DUX4 sarcoma (CDS) is a rare but highly aggressive undifferentiated small round cell sarcoma driven by a fusion between the tumor suppressor Capicua (CIC) and DUX4. Currently, there are no effective treatments and efforts to identify and translate better therapies are limited by the scarcity of patient tumor samples and cell lines. To address this limitation, we generated three genetically engineered mouse models of CDS (Ch7CDS, Ai9CDS, and TOPCDS). Remarkably, chimeric mice from all three conditional models developed spontaneous soft tissue tumors and disseminated disease in the absence of Cre-recombinase. The penetrance of spontaneous (Cre-independent) tumor formation was complete irrespective of bi-allelic Cic function and the distance between adjacent loxP sites. Characterization of soft tissue and presumed metastatic tumors showed that they consistently expressed the CIC::DUX4 fusion protein and many downstream markers of the disease credentialing the models as CDS. In addition, tumor-derived cell lines were generated and ChIP-seq was preformed to map fusion-gene specific binding using an N-terminal HA epitope tag. These datasets, along with paired H3K27ac ChIP-sequencing maps, validate CIC::DUX4 as a neomorphic transcriptional activator. Moreover, they are consistent with a model where ETS family transcription factors are cooperative and redundant drivers of the core regulatory circuitry in CDS.


Subject(s)
Sarcoma, Small Cell , Sarcoma , Soft Tissue Neoplasms , Animals , Mice , Alleles , Biomarkers, Tumor , Oncogene Proteins, Fusion/genetics , Oncogene Proteins, Fusion/metabolism , Proto-Oncogene Proteins c-ets , Sarcoma/genetics , Sarcoma/metabolism , Sarcoma, Small Cell/chemistry , Sarcoma, Small Cell/genetics , Soft Tissue Neoplasms/genetics , Soft Tissue Neoplasms/pathology , Humans
5.
J Affect Disord ; 351: 631-640, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38290583

ABSTRACT

We examine structural brain characteristics across three diagnostic categories: at risk for serious mental illness; first-presenting episode and recurrent major depressive disorder (MDD). We investigate whether the three diagnostic groups display a stepwise pattern of brain changes in the cortico-limbic regions. Integrated clinical and neuroimaging data from three large Canadian studies were pooled (total n = 622 participants, aged 12-66 years). Four clinical profiles were used in the classification of a clinical staging model: healthy comparison individuals with no history of depression (HC, n = 240), individuals at high risk for serious mental illness due to the presence of subclinical symptoms (SC, n = 80), first-episode depression (FD, n = 82), and participants with recurrent MDD in a current major depressive episode (RD, n = 220). Whole-brain volumetric measurements were extracted with FreeSurfer 7.1 and examined using three different types of analyses. Hippocampal volume decrease and cortico-limbic thinning were the most informative features for the RD vs HC comparisons. FD vs HC revealed that FD participants were characterized by a focal decrease in cortical thickness and global enlargement in amygdala volumes. Greater total amygdala volumes were significantly associated with earlier onset of illness in the FD but not the RD group. We did not confirm the construct validity of a tested clinical staging model, as a differential pattern of brain alterations was identified across the three diagnostic groups that did not parallel a stepwise clinical staging approach. The pathological processes during early stages of the illness may fundamentally differ from those that occur at later stages with clinical progression.


Subject(s)
Depressive Disorder, Major , Humans , Depressive Disorder, Major/diagnostic imaging , Depressive Disorder, Major/pathology , Depression , Magnetic Resonance Imaging/methods , Canada , Neuroimaging
6.
J Adv Res ; 2024 Jan 26.
Article in English | MEDLINE | ID: mdl-38280715

ABSTRACT

INTRODUCTION: Small-molecule Programmable Cell Death Protein 1/Programmable Death-Ligand 1 (PD1/PDL1) inhibition via PDL1 dimerization has the potential to lead to inexpensive drugs with better cancer patient outcomes and milder side effects. However, this therapeutic approach has proven challenging, with only one PDL1 dimerizer reaching early clinical trials so far. There is hence a need for fast and accurate methods to develop alternative PDL1 dimerizers. OBJECTIVES: We aim to show that structure-based virtual screening (SBVS) based on PDL1-specific machine-learning (ML) scoring functions (SFs) is a powerful drug design tool for detecting PD1/PDL1 inhibitors via PDL1 dimerization. METHODS: By incorporating the latest MLSF advances, we generated and evaluated PDL1-specific MLSFs (classifiers and inactive-enriched regressors) on two demanding test sets. RESULTS: 60 PDL1-specific MLSFs (30 classifiers and 30 regressors) were generated. Our large-scale analysis provides highly predictive PDL1-specific MLSFs that benefitted from training with large volumes of docked inactives and enabling inactive-enriched regression. CONCLUSION: PDL1-specific MLSFs strongly outperformed generic SFs of various types on this target and are released here without restrictions.

7.
Nature ; 624(7991): 252, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38086935
8.
Nat Protoc ; 18(11): 3460-3511, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37845361

ABSTRACT

Structure-based virtual screening (SBVS) via docking has been used to discover active molecules for a range of therapeutic targets. Chemical and protein data sets that contain integrated bioactivity information have increased both in number and in size. Artificial intelligence and, more concretely, its machine-learning (ML) branch, including deep learning, have effectively exploited these data sets to build scoring functions (SFs) for SBVS against targets with an atomic-resolution 3D model (e.g., generated by X-ray crystallography or predicted by AlphaFold2). Often outperforming their generic and non-ML counterparts, target-specific ML-based SFs represent the state of the art for SBVS. Here, we present a comprehensive and user-friendly protocol to build and rigorously evaluate these new SFs for SBVS. This protocol is organized into four sections: (i) using a public benchmark of a given target to evaluate an existing generic SF; (ii) preparing experimental data for a target from public repositories; (iii) partitioning data into a training set and a test set for subsequent target-specific ML modeling; and (iv) generating and evaluating target-specific ML SFs by using the prepared training-test partitions. All necessary code and input/output data related to three example targets (acetylcholinesterase, HMG-CoA reductase, and peroxisome proliferator-activated receptor-α) are available at https://github.com/vktrannguyen/MLSF-protocol , can be run by using a single computer within 1 week and make use of easily accessible software/programs (e.g., Smina, CNN-Score, RF-Score-VS and DeepCoy) and web resources. Our aim is to provide practical guidance on how to augment training data to enhance SBVS performance, how to identify the most suitable supervised learning algorithm for a data set, and how to build an SF with the highest likelihood of discovering target-active molecules within a given compound library.


Subject(s)
Acetylcholinesterase , Artificial Intelligence , Ligands , Machine Learning , Algorithms , Molecular Docking Simulation
9.
Cancer Res ; 83(23): 3846-3860, 2023 12 01.
Article in English | MEDLINE | ID: mdl-37819236

ABSTRACT

NUT carcinoma (NC) is an aggressive squamous carcinoma defined by the BRD4-NUT fusion oncoprotein. Routinely effective systemic treatments are unavailable for most NC patients. The lack of an adequate animal model precludes identifying and leveraging cell-extrinsic factors therapeutically in NC. Here, we created a genetically engineered mouse model (GEMM) of NC that forms a Brd4::NUTM1 fusion gene upon tamoxifen induction of Sox2-driven Cre. The model displayed complete disease penetrance, with tumors arising from the squamous epithelium weeks after induction and all mice succumbing to the disease shortly thereafter. Closely resembling human NC (hNC), GEMM tumors (mNC) were poorly differentiated squamous carcinomas with high expression of MYC that metastasized to solid organs and regional lymph nodes. Two GEMM-derived cell lines were developed whose transcriptomic and epigenetic landscapes harbored key features of primary GEMM tumors. Importantly, GEMM tumor and cell line transcriptomes co-classified with those of human NC. BRD4-NUT also blocked differentiation and maintained the growth of mNC as in hNC. Mechanistically, GEMM primary tumors and cell lines formed large histone H3K27ac-enriched domains, termed megadomains, that were invariably associated with the expression of key NC-defining proto-oncogenes, Myc and Trp63. Small-molecule BET bromodomain inhibition (BETi) of mNC induced differentiation and growth arrest and prolonged survival of NC GEMMs, as it does in hNC models. Overall, tumor formation in the NC GEMM is definitive evidence that BRD4-NUT alone can potently drive the malignant transformation of squamous progenitor cells into NC. SIGNIFICANCE: The development of an immunocompetent model of NUT carcinoma that closely mimics the human disease provides a valuable global resource for mechanistic and preclinical studies to improve treatment of this incurable disease.


Subject(s)
Carcinoma, Squamous Cell , Transcription Factors , Animals , Humans , Mice , Carcinoma, Squamous Cell/pathology , Cell Cycle Proteins/genetics , Cell Transformation, Neoplastic/genetics , Nuclear Proteins/metabolism , Oncogene Proteins, Fusion/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
10.
Biomater Sci ; 11(17): 5797-5808, 2023 Aug 22.
Article in English | MEDLINE | ID: mdl-37401742

ABSTRACT

The delivery of genetic material (DNA and RNA) to cells can cure a wide range of diseases but is limited by the delivery efficiency of the carrier system. Poly ß-amino esters (pBAEs) are promising polymer-based vectors that form polyplexes with negatively charged oligonucleotides, enabling cell membrane uptake and gene delivery. pBAE backbone polymer chemistry, as well as terminal oligopeptide modifications, define cellular uptake and transfection efficiency in a given cell line, along with nanoparticle size and polydispersity. Moreover, uptake and transfection efficiency of a given polyplex formulation also vary from cell type to cell type. Therefore, finding the optimal formulation leading to high uptake in a new cell line is dictated by trial and error, and requires time and resources. Machine learning (ML) is an ideal in silico screening tool to learn the non-linearities of complex data sets, like the one presented herein, with the aim of predicting cellular internalisation of pBAE polyplexes. A library of pBAE nanoparticles was fabricated and the uptake studied in 4 different cell lines, on which various ML models were successfully trained. The best performing models were found to be gradient-boosted trees and neural networks. The gradient-boosted trees model was then analysed using SHapley Additive exPlanations, to interpret the model and gain an understanding into the important features and their impact on the predicted outcome.


Subject(s)
Nanoparticles , Polymers , Transfection , DNA , Gene Transfer Techniques , Cell Line
11.
J Med Internet Res ; 25: e49323, 2023 05 31.
Article in English | MEDLINE | ID: mdl-37256656

ABSTRACT

Májovský and colleagues have investigated the important issue of ChatGPT being used for the complete generation of scientific works, including fake data and tables. The issues behind why ChatGPT poses a significant concern to research reach far beyond the model itself. Once again, the lack of reproducibility and visibility of scientific works creates an environment where fraudulent or inaccurate work can thrive. What are some of the ways in which we can handle this new situation?


Subject(s)
Artificial Intelligence , Software , Humans , Reproducibility of Results
12.
Biomolecules ; 13(3)2023 03 08.
Article in English | MEDLINE | ID: mdl-36979433

ABSTRACT

Machine learning-based models have been widely used in the early drug-design pipeline. To validate these models, cross-validation strategies have been employed, including those using clustering of molecules in terms of their chemical structures. However, the poor clustering of compounds will compromise such validation, especially on test molecules dissimilar to those in the training set. This study aims at finding the best way to cluster the molecules screened by the National Cancer Institute (NCI)-60 project by comparing hierarchical, Taylor-Butina, and uniform manifold approximation and projection (UMAP) clustering methods. The best-performing algorithm can then be used to generate clusters for model validation strategies. This study also aims at measuring the impact of removing outlier molecules prior to the clustering step. Clustering results are evaluated using three well-known clustering quality metrics. In addition, we compute an average similarity matrix to assess the quality of each cluster. The results show variation in clustering quality from method to method. The clusters obtained by the hierarchical and Taylor-Butina methods are more computationally expensive to use in cross-validation strategies, and both cluster the molecules poorly. In contrast, the UMAP method provides the best quality, and therefore we recommend it to analyze this highly valuable dataset.


Subject(s)
Algorithms , Machine Learning , United States , National Cancer Institute (U.S.) , Cluster Analysis , Drug Design
13.
J Chem Inf Model ; 63(5): 1401-1405, 2023 03 13.
Article in English | MEDLINE | ID: mdl-36848585

ABSTRACT

We discuss how data unbiasing and simple methods such as protein-ligand Interaction FingerPrint (IFP) can overestimate virtual screening performance. We also show that IFP is strongly outperformed by target-specific machine-learning scoring functions, which were not considered in a recent report concluding that simple methods were better than machine-learning scoring functions at virtual screening.


Subject(s)
Ligands , Proteins , Proteins/chemistry , Machine Learning
14.
Compr Psychiatry ; 122: 152377, 2023 04.
Article in English | MEDLINE | ID: mdl-36787672

ABSTRACT

BACKGROUND: Despite limited clinical evidence of its efficacy, cannabis use has been commonly reported for the management of various mental health concerns in naturalistic field studies. The aim of the current study was to use machine learning methods to investigate predictors of perceived symptom change across various mental health symptoms with acute cannabis use in a large naturalistic sample. METHODS: Data from 68,819 unique observations of cannabis use from 1307 individuals using cannabis to manage mental health symptoms were analyzed. Data were extracted from Strainprint®, a mobile app that allows users to monitor their cannabis use for therapeutic purposes. Machine learning models were employed to predict self-perceived symptom change after cannabis use, and SHapley Additive exPlanations (SHAP) value plots were used to assess feature importance of individual predictors in the model. Interaction effects of symptom severity pre-scores of anxiety, depression, insomnia, and gender were also examined. RESULTS: The factors that were most strongly associated with perceived symptom change following acute cannabis use were pre-symptom severity, age, gender, and the ratio of CBD to THC. Further examination on the impact of baseline severity for the most commonly reported symptoms revealed distinct responses, with cannabis being reported to more likely benefit individuals with lower pre-symptom severity for depression, and higher pre-symptom severity for insomnia. Responses to cannabis use also differed between genders. CONCLUSIONS: Findings from this study highlight the importance of several factors in predicting perceived symptom change with acute cannabis use for mental health symptom management. Mental health profiles and baseline symptom severity may play a large role in perceived responses to cannabis. Distinct response patterns were also noted across commonly reported mental health symptoms, emphasizing the need for placebo-controlled cannabis trials for specific user profiles.


Subject(s)
Cannabis , Sleep Initiation and Maintenance Disorders , Humans , Male , Female , Mental Health , Anxiety/therapy , Anxiety Disorders
15.
Schizophrenia (Heidelb) ; 9(1): 3, 2023 Jan 09.
Article in English | MEDLINE | ID: mdl-36624107

ABSTRACT

Neuroimaging-based brain age is a biomarker that is generated by machine learning (ML) predictions. The brain age gap (BAG) is typically defined as the difference between the predicted brain age and chronological age. Studies have consistently reported a positive BAG in individuals with schizophrenia (SCZ). However, there is little understanding of which specific factors drive the ML-based brain age predictions, leading to limited biological interpretations of the BAG. We gathered data from three publicly available databases - COBRE, MCIC, and UCLA - and an additional dataset (TOPSY) of early-stage schizophrenia (82.5% untreated first-episode sample) and calculated brain age with pre-trained gradient-boosted trees. Then, we applied SHapley Additive Explanations (SHAP) to identify which brain features influence brain age predictions. We investigated the interaction between the SHAP score for each feature and group as a function of the BAG. These analyses identified total gray matter volume (group × SHAP interaction term ß = 1.71 [0.53; 3.23]; pcorr < 0.03) as the feature that influences the BAG observed in SCZ among the brain features that are most predictive of brain age. Other brain features also presented differences in SHAP values between SCZ and HC, but they were not significantly associated with the BAG. We compared the findings with a non-psychotic depression dataset (CAN-BIND), where the interaction was not significant. This study has important implications for the understanding of brain age prediction models and the BAG in SCZ and, potentially, in other psychiatric disorders.

16.
J Psychiatr Res ; 157: 168-173, 2023 01.
Article in English | MEDLINE | ID: mdl-36470198

ABSTRACT

Prior studies have found an especially high prevalence of illicit substance use among adolescents and young adults in Brazil. The current study aimed to employ machine learning techniques to identify predictors of illicit substance abuse/dependence among a large community sample of young adults followed for 5 years. This prospective, population-based cohort study included a sample of young adults between the ages of 18-24 years from Pelotas, Brazil at baseline (T1). The Alcohol, Smoking and Substance Involvement Screening Test (ASSIST) was used to assess illicit substance abuse/dependence. A clinical interview was conducted to collect data on sociodemographic characteristics and psychopathology. Elastic net was used to generate a regularized linear model for the machine learning component of this study, which followed standard machine learning protocols. A total of 1560 young adults were assessed at T1, while 1244 were reassessed at the 5-year follow-up period (T2). The strongest predictors of illicit substance abuse/dependence at baseline (AUC of 0.83) were alcohol abuse/dependence, tobacco abuse/dependence, being in a current major depressive episode, history of a lifetime manic episode, current suicide risk, and male sex. The strongest predictors for illicit substance abuse/dependence at the 5-year follow-up (AUC: 0.79) were tobacco abuse/dependence at T1, history of a lifetime manic episode at T1, male sex, alcohol abuse/dependence at T1, and current suicide risk at T1. Our findings indicate that machine learning techniques hold the potential to predict illicit substance abuse/dependence among young adults using sociodemographic/clinical characteristics, with relatively high accuracy.


Subject(s)
Alcoholism , Depressive Disorder, Major , Substance-Related Disorders , Tobacco Use Disorder , Adolescent , Young Adult , Humans , Male , Adult , Alcoholism/epidemiology , Cohort Studies , Prospective Studies , Mania , Substance-Related Disorders/epidemiology , Tobacco Use Disorder/epidemiology
17.
Transl Psychiatry ; 12(1): 470, 2022 Nov 09.
Article in English | MEDLINE | ID: mdl-36347838

ABSTRACT

Although reducing criminal outcomes in individuals with mental illness have long been a priority for governments worldwide, there is still a lack of objective and highly accurate tools that can predict these events at an individual level. Predictive machine learning models may provide a unique opportunity to identify those at the highest risk of criminal activity and facilitate personalized rehabilitation strategies. Therefore, this systematic review and meta-analysis aims to describe the diagnostic accuracy of studies using machine learning techniques to predict criminal and violent outcomes in psychiatry. We performed meta-analyses using the mada, meta, and dmetatools packages in R to predict criminal and violent outcomes in psychiatric patients (n = 2428) (Registration Number: CRD42019127169) by searching PubMed, Scopus, and Web of Science for articles published in any language up to April 2022. Twenty studies were included in the systematic review. Overall, studies used single-nucleotide polymorphisms, text analysis, psychometric scales, hospital records, and resting-state regional cerebral blood flow to build predictive models. Of the studies described in the systematic review, nine were included in the present meta-analysis. The area under the curve (AUC) for predicting violent and criminal outcomes in psychiatry was 0.816 (95% Confidence Interval (CI): 70.57-88.15), with a partial AUC of 0.773, and average sensitivity of 73.33% (95% CI: 64.09-79.63), and average specificity of 72.90% (95% CI: 63.98-79.66), respectively. Furthermore, the pooled accuracy across models was 71.45% (95% CI: 60.88-83.86), with a tau squared (τ2) of 0.0424 (95% CI: 0.0184-0.1553). Based on available evidence, we suggest that prospective models include evidence-based risk factors identified in prior actuarial models. Moreover, there is a need for a greater emphasis on identifying biological features and incorporating novel variables which have not been explored in prior literature. Furthermore, available models remain preliminary, and prospective validation with independent datasets, and across cultures, will be required prior to clinical implementation. Nonetheless, predictive machine learning models hold promise in providing clinicians and researchers with actionable tools to improve how we prevent, detect, or intervene in relevant crime and violent-related outcomes in psychiatry.


Subject(s)
Criminals , Mental Disorders , Psychiatry , Humans , Aggression , Mental Disorders/diagnosis , Area Under Curve
18.
Adv Sci (Weinh) ; 9(24): e2201501, 2022 08.
Article in English | MEDLINE | ID: mdl-35785523

ABSTRACT

Doxorubicin is a common treatment for breast cancer. However, not all patients respond to this drug, which sometimes causes life-threatening side effects. Accurately anticipating doxorubicin-resistant patients would therefore permit to spare them this risk while considering alternative treatments without delay. Stratifying patients based on molecular markers in their pretreatment tumors is a promising approach to advance toward this ambitious goal, but single-gene gene markers such as HER2 expression have not shown to be sufficiently predictive. The recent availability of matched doxorubicin-response and diverse molecular profiles across breast cancer patients permits now analysis at a much larger scale. 16 machine learning algorithms and 8 molecular profiles are systematically evaluated on the same cohort of patients. Only 2 of the 128 resulting models are substantially predictive, showing that they can be easily missed by a standard-scale analysis. The best model is classification and regression tree (CART) nonlinearly combining 4 selected miRNA isoforms to predict doxorubicin response (median Matthew correlation coefficient (MCC) and area under the curve (AUC) of 0.56 and 0.80, respectively). By contrast, HER2 expression is significantly less predictive (median MCC and AUC of 0.14 and 0.57, respectively). As the predictive accuracy of this CART model increases with larger training sets, its update with future data should result in even better accuracy.


Subject(s)
Breast Neoplasms , MicroRNAs , Algorithms , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Doxorubicin/therapeutic use , Female , Humans , Machine Learning , MicroRNAs/genetics
19.
Bipolar Disord ; 24(6): 580-614, 2022 09.
Article in English | MEDLINE | ID: mdl-35839276

ABSTRACT

BACKGROUND: The clinical effects of smartphone-based interventions for bipolar disorder (BD) have yet to be established. OBJECTIVES: To examine the efficacy of smartphone-based interventions in BD and how the included studies reported user-engagement indicators. METHODS: We conducted a systematic search on January 24, 2022, in PubMed, Scopus, Embase, APA PsycINFO, and Web of Science. We used random-effects meta-analysis to calculate the standardized difference (Hedges' g) in pre-post change scores between smartphone intervention and control conditions. The study was pre-registered with PROSPERO (CRD42021226668). RESULTS: The literature search identified 6034 studies. Thirteen articles fulfilled the selection criteria. We included seven RCTs and performed meta-analyses comparing the pre-post change in depressive and (hypo)manic symptom severity, functioning, quality of life, and perceived stress between smartphone interventions and control conditions. There was significant heterogeneity among studies and no meta-analysis reached statistical significance. Results were also inconclusive regarding affective relapses and psychiatric readmissions. All studies reported positive user-engagement indicators. CONCLUSION: We did not find evidence to support that smartphone interventions may reduce the severity of depressive or manic symptoms in BD. The high heterogeneity of studies supports the need for expert consensus to establish ideally how studies should be designed and the use of more sensitive outcomes, such as affective relapses and psychiatric hospitalizations, as well as the quantification of mood instability. The ISBD Big Data Task Force provides preliminary recommendations to reduce the heterogeneity and achieve more valid evidence in the field.


Subject(s)
Bipolar Disorder , Smartphone , Big Data , Bipolar Disorder/psychology , Humans , Quality of Life , Recurrence
20.
Med. paliat ; 29(3): 201-210, jul.-sep. 2022. ilus, tab
Article in Spanish | IBECS | ID: ibc-213597

ABSTRACT

Introducción: La esclerosis lateral amiotrófica (ELA) se define por la degeneración progresiva de las motoneuronas superiores e inferiores, lo que provoca una debilidad muscular progresiva que amenaza gravemente la autonomía motora, la comunicación oral, la deglución y la respiración. Estas características hacen que la ELA sea una de las enfermedades más duras emocionalmente para los y las pacientes y sus familiares y personas cuidadoras. La persona con ELA y la familia se pueden beneficiar de los cuidados paliativos en las etapas tempranas de la enfermedad, no solo para planificar una buena muerte cuando corresponda, sino para beneficiarse de tratamientos especializados a cualquier edad y en cualquier estadio de la enfermedad.Objetivo: El objetivo de esta revisión es actualizar y organizar el conocimiento sobre las necesidades paliativas psicosociales de las personas con ELA y cuidadoras, con el fi n de mejorar protocolos de tratamiento y la implementación de planes integrales de cuidados paliativos. Material y métodos: Para ello se realizó una búsqueda en PubMed y Cochrane y en la revista Medicina Paliativa de artículos de revisión sobre ELA y cuidados paliativos. Resultados: Se identificaron 5 estudios que cumplían criterios de inclusión con abundante información sobre necesidades psicosociales de las personas con ELA y cuidadoras, que recorren todo el proceso de la enfermedad, desde el diagnóstico hasta el duelo. Los resultados se clasifican en base a un triple eje: I. Naturaleza de la necesidad; II. Etapa de la enfermedad y III. Persona cuidadora o enferma. Conclusiones: Los beneficios de los cuidados paliativos en la ELA requieren una consideración complementaria a los de la neurología desde el diagnóstico hasta el duelo. (AU)


Introduction: Amyotrophic lateral sclerosis (ALS) is defined by a progressive degeneration of the upper and lower motor neurons resulting in progressive muscle weakness, which severely compromises motor autonomy, oral communication, swallowing, and breathing. These characteristics make ALS one of the most emotionally difficult diseases for patients and their families, as well as their caregivers. The patient and his/her family can benefit from palliative care in the early stages of the disease, not only to plan for a good death when appropriate but also to benefit from specialized treatments at any age and any stage of the disease.Objective: The aim of this review was to update and organize the extant knowledge about the psychosocial palliative needs of patients and caregivers in order to improve treatment protocols and the implementation of comprehensive palliative care plans. Material and methods: To this end, we searched PubMed and Cochrane and the journal Palliative Medicine for review articles on ALS and palliative care. Results: Five studies that met inclusion criteria were identified with a wealth of information on the psychosocial needs of patients and caregivers, covering the entire disease process from diagnosis to bereavement. The results are classified on the basis of a threefold axis: I. Nature of the need; II. Stage of the illness; and III. Caregiver or sick person. Conclusion: The conclusion is that the benefits of palliative care in ALS require complementary consideration to those of neurology from diagnosis to bereavement. (AU)


Subject(s)
Humans , Amyotrophic Lateral Sclerosis , Palliative Care , Family , Caregivers
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