Autoregressive Point-Processes as Latent State-Space Models: a Moment-Closure Approach to Fluctuations and Autocorrelations

Modeling and interpreting spike train data is a task of central importance in computational neuroscience, with significant translational implications. Two popular classes of data-driven models for this task are autoregressive Point Process Generalized Linear models (PPGLM) and latent State-Space models (SSM) with point-process observations. In this letter, we derive a mathematical connection between these two classes of models. By introducing an auxiliary history process, we represent exactly a PPGLM in terms of a latent, infinite dimensional dynamical system, which can then be mapped onto an SSM by basis function projections and moment closure. This representation provides a new perspective on widely used methods for modeling spike data, and also suggests novel algorithmic approaches to fitting such models. We illustrate our results on a phasic bursting neuron model, showing that our proposed approach provides an accurate and efficient way to capture neural dynamics

Machine Learning Approach to Predict Clinical Pregnancy Potential in Women Undergoing IVF Program

Objective: Hidden knowledge could be discovered within a large practical data of in vitro fertilization (IVF) practice. In this study, Machine learning–based data mining techniques were utilized to construct a reliable prediction model for clinical pregnancy in IVF. Study Design: A retrospective cohort multicenter study involving 4.570 IVF cycles. All patients underwent fresh embryo transfer at either the cleavage or blastocyst stage between January 2015 and December 2019. The experiment focused on utilizing tree-based classifiers to generate and compare the most effective prediction model that could predict a clinical pregnancy through clinical data. Additionally, each classifier is optimized via a genetic algorithm technique, along with the selection of variables. Results: Both the decision tree and random forest showed similar performance that was much better than the gradient boost. The two superior classifiers achieved a balanced accuracy of roughly 0.62. Additionally, each prediction model was shown to work optimally with different combinations of variables, with some variables being consistently included, such as female age, and some consistently excluded, which provides an insight into the relationship between the variables and each prediction model. Conclusion: Machine learning algorithm remains effective for the purpose of data mining and knowledge extraction in IVF clinical datasets through which a relatively reliable prediction system for clinical pregnancy could be constructed, provided the available data is sufficient. Keywords: In Vitro Fertilization; Prediction Model; Decision Tree; Machine Learning; Artificial Intelligenc

Embryo ploidy status classification through computer-assisted morphology assessment

BACKGROUND: Preimplantation genetic testing for aneuploidy has been proven to be effective in determining the embryo’s chromosomal or ploidy status. The test requires a biopsy of embryonic cells on day 3, 5, or 6 from which complete information on the chromosomes would be obtained. The main drawbacks of preimplantation genetic testing for aneuploidy include its relatively invasive approach and the lack of research studies on the long-term effects of preimplantation genetic testing for aneuploidy. OBJECTIVE: Computer-assisted predictive modeling through machine learning and deep learning algorithms has been proposed to minimize the use of invasive preimplantation genetic testing for aneuploidy. The capability to predict morphologic characteristics of embryo ploidy status creates a meaningful support system for decision-making before further treatment. STUDY DESIGN: Image processing is a component in developing a predictive model specialized in image classification through which a model is able to differentiate images based on unique features. Image processing is obtained through image augmentation to capture segmented embryos and perform feature extraction. Furthermore, multiple machine learning and deep learning algorithms were used to create prediction- based modeling, and all of the prediction models undergo similar model performance assessments to determine the best model prediction algorithm. RESULTS: An efficient artificial intelligence model that can predict embryo ploidy status was developed using image processing through a his- togram of oriented gradient and then followed by principal component analysis. The gradient boosting algorithm showed an advantage against other algorithms and yielded an accuracy of 0.74, an aneuploid precision of 0.83, and an aneuploid predictive value (recall) of 0.84. CONCLUSION: This research study proved that machine-assisted technology perceives the embryo differently than human observation and determined that further research on in vitro fertilization is needed. The study finding serves as a basis for developing a better computer-assisted prediction model. Key words: artificial intelligence, image processing, in vitro fertilization, noninvasive embryo assessment, preimplantation genetic testing for aneuploid, ploidy status, prediction mode

Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer

open20Women treated for breast cancer (BC) are at risk of developing secondary tumors, such as lung cancer (LC). Since rare germline variants have been linked to multiple cancer development, we hypothesized that BC survivors might be prone to develop LC as a result of harboring rare variants. Sixty patients with LC with previous BC (the study population; SP) and 53 women with either BC or LC and no secondary cancer (control population; CP) were enrolled. Whole exome sequencing was performed in both tumors and unaffected tissues from 28/60 SP patients, and in germline DNA from 32/53 CP. Candidate genes were validated in the remaining individuals from both populations. We found two main mutational signature profiles: S1 (C>T) in all BCs and 16/28 LCs, and S2 (C>A) which is strongly associated with smoking, in 12/28 LCs. The burden test over rare germline variants in S1-LC vs CP identified 248 genes. Validation confirmed GSN as significantly associated with LC in never-smokers. In conclusion, our data suggest two signatures involved in LC onset in women with previous BC. One of these signatures is linked to smoking. Conversely, regardless of smoking habit, in a subgroup of BC survivors genetic susceptibility may contribute to LC risk.openCoco, Simona; Bonfiglio, Silvia; Cittaro, Davide; Vanni, Irene; Mora, Marco; Genova, Carlo; Dal Bello, Maria Giovanna; Boccardo, Simona; Alama, Angela; Rijavec, Erika; Sini, Claudio; Rossella, Valeria; Barletta, Giulia; Biello, Federica; Truini, Anna; Bruzzo, Cristina; Gallo, Maurizio; Lazarevic, Dejan; Ballestrero, Alberto; Grossi, FrancescoCoco, Simona; Bonfiglio, Silvia; Cittaro, Davide; Vanni, Irene; Mora, Marco; Genova, Carlo; Dal Bello, Maria Giovanna; Boccardo, Simona; Alama, Angela; Rijavec, Erika; Sini, Claudio; Rossella, Valeria; Barletta, Giulia; Biello, Federica; Truini, Anna; Bruzzo, Cristina; Gallo, Maurizio; Lazarevic, Dejan; Ballestrero, Alberto; Grossi, Francesc

Sotorasib in KRASp.G12C mutated advanced NSCLC: Real-world data from the Italian expanded access program

Background: Sotorasib showed a significant improvement of progression free survival (PFS), safety and quality of life over docetaxel in patients with KRASp.G12C-mutated advanced non-small-cell lung cancer (NSCLC) within the CodeBreak-200 study. Here we report real-world efficacy and tolerability data from NSCLC patients who received sotorasib within the Italian expanded access program (EAP). Methods: Sotorasib (960 mg, orally, once daily) was available on physician request for KRASp.G12C mutant advanced NSCLC patients. Clinical-pathological and molecular data were collected from the Italian ATLAS real-world registry. Patients underwent CT-scan and responses were evaluated by RECIST criteria. Efficacy and tolerability outcomes have been assessed. Results: A total of 196 advanced NSCLC patients were treated across 30 Italian centers. Median age was 69 years old (range 33-86). Most patients were male (61 %), former (49 %) or current smokers (43 %), with ECOG-PS 0/1 (84 %) and adenocarcinoma subtype (90 %). 45 % and 32 % of patients received sotorasib in 2nd and 3rd line, respectively. Overall, response rate was 26 % and the median duration of response was 5.7 months (95 % CI: 4.4-7.0). Median PFS and OS were 5.8 months (95 % CI: 5 - 6.5) and 8.2 months (95 % CI: 6.3 - 9.9). Grade 3-4 TRAEs occurred in 16.5 % of patients, with Grade >= 3 liver enzyme increase and TRAEs-related discontinuation reported in 12 % and 4.6 % of cases. Conclusion: Real-world data from the Italian EAP confirm the tolerability and effectiveness of sotorasib in patients with KRASp.G12C-mutated advanced NSCLC and highlight the value of the national ATLAS network as source of real-world evidence driving the clinical management of NSCLC patients

Expression of Ribonucleotide Reductase Subunit-2 and Thymidylate Synthase Correlates with Poor Prognosis in Patients with Resected Stages I–III Non-Small Cell Lung Cancer

Biomarkers can help to identify patients with early-stages or locally advanced non-small cell lung cancer (NSCLC) who have high risk of relapse and poor prognosis. To correlate the expression of seven biomarkers involved in DNA synthesis and repair and in cell division with clinical outcome, we consecutively collected 82 tumour tissues from radically resected NSCLC patients. The following biomarkers were investigated using IHC and qRT-PCR: excision repair cross-complementation group 1 (ERCC1), breast cancer 1 (BRCA1), ribonucleotide reductase subunits M1 and M2 (RRM1 and RRM2), subunit p53R2, thymidylate synthase (TS), and class III beta-tubulin (TUBB3). Gene expression levels were also validated in an available NSCLC microarray dataset. Multivariate analysis identified the protein overexpression of RRM2 and TS as independent prognostic factors of shorter overall survival (OS). Kaplan-Meier analysis showed a trend in shorter OS for patients with RRM2, TS, and ERCC1, BRCA1 overexpressed tumours. For all of the biomarkers except TUBB3, the OS trends relative to the gene expression levels were in agreement with those relative to the protein expression levels. The NSCLC microarray dataset showed RRM2 and TS as biomarkers significantly associated with OS. This study suggests that high expression levels of RRM2 and TS might be negative prognostic factors for resected NSCLC patients

Precision Medicine for NSCLC in the Era of Immunotherapy: New Biomarkers to Select the Most Suitable Treatment or the Most Suitable Patient

In recent years, the evolution of treatments has made it possible to significantly improve the outcomes of patients with non-small cell lung cancer (NSCLC). In particular, while molecular targeted therapies are effective in specific patient sub-groups, immune checkpoint inhibitors (ICIs) have greatly influenced the outcomes of a large proportion of NSCLC patients. While nivolumab activity was initially assessed irrespective of predictive biomarkers, subsequent pivotal studies involving other PD-1/PD-L1 inhibitors in pre-treated advanced NSCLC (atezolizumab within the OAK study and pembrolizumab in the Keynote 010 study) reported the first correlations between clinical outcomes and PD-L1 expression. However, PD-L1 could not be sufficient on its own to select patients who may benefit from immunotherapy. Many studies have tried to discover more precise markers that are derived from tumor tissue or from peripheral blood. This review aims to analyze any characteristics of the immunogram that could be used as a predictive biomarker for response to ICIs. Furthermore, we describe the most important genetic alteration that might predict the activity of immunotherapy