Predicting drug solubility in organic solvents mixtures: A machine-learning approach supported by high-throughput experimentation.

A novel approach based on supervised machine-learning is proposed to predict the solubility of drugs and drug-like molecules in mixtures of organic solvents. Similar to quantitative structure-property relationship (QSPR) models, different solvent types are identified by molecular descriptors, which, in this study, are considered as UNIFAC subgroups. To overcome the potential lack of UNIFAC subgroups for the complex Active Pharmaceutical Ingredients (APIs) currently developed in the pharmaceutical industry, the API molecule is considered as a unique entity in the proposed modelling approach. Therefore, API solubility is predicted as a function of temperature, functional subgroups of the solvents and composition of the solvent mixture; in turn, regressors' correlation is handled through Partial Least-Squares (PLS) regression. The method is developed and tested with experimental data of a real API and 14 organic solvents that are industrially employed for crystallisation. Solubility predictions are accurate and precise for single solvents, binary mixtures and ternary mixtures of organic solvents at different compositions and temperatures, with a determination coefficient R2 ≥ 0.90. To further test the applicability of the model, the proposed approach is applied to 9 literature organic solubility datasets of drugs and drug-like compounds and compared to benchmark solubility models in the literature. Results show that the proposed approach provides satisfactory predictions: the majority of validation and calibration data have R2 = 0.95-0.99; the ratio between RMSE (root mean squared error) of the proposed method and the range of measured solubility values is from 1 to 3 orders of magnitude smaller than the RMSE ratio obtained by the benchmark models.

Promoting the preservation of strawberry by supercritical CO2 drying.

This work aimed to investigate the supercritical CO2 (ScCO2) drying of strawberries and its effect on enzymatic, chemical and microbial stability. Process conditions influenced the final weight loss (WL), water activity (aw) and the inactivation of polyphenol oxidase (PPO) and peroxidase (POD). At 40 °C, an efficient drying (WL > 92 %, aw < 0.34) and a complete enzymatic (POD and PPO activity) inactivation can be achieved using several combinations of pressure, time and flow rate. ScCO2 dried strawberry at 40 °C, 13.3 MPa, 7 h and 19 kg/h flow rate maintain the total content of Vitamin C (358.5 mg/100 g), 95 % of total anthocyanin (61.68 mg/100 g) and 76 % of total flavonoids (25.85 mg/100 g) in comparison with fresh samples. Foodborne pathogens (E.coli O157:H7, Salmonella enterica and Listeria monocytogenes) inoculated at high concentration (≥6 log CFU/g) were undetected after the process. Overall results are promising for the development of a novel low temperature drying process for the production of healthy and safe snack.

Feature Selection and Molecular Classification of Cancer Phenotypes: A Comparative Study.

The classification of high dimensional gene expression data is key to the development of effective diagnostic and prognostic tools. Feature selection involves finding the best subset with the highest power in predicting class labels. Here, we conducted a comparative study focused on different combinations of feature selectors (Chi-Squared, mRMR, Relief-F, and Genetic Algorithms) and classification learning algorithms (Random Forests, PLS-DA, SVM, Regularized Logistic/Multinomial Regression, and kNN) to identify those with the best predictive capacity. The performance of each combination is evaluated through an empirical study on three benchmark cancer-related microarray datasets. Our results first suggest that the quality of the data relevant to the target classes is key for the successful classification of cancer phenotypes. We also proved that, for a given classification learning algorithm and dataset, all filters have a similar performance. Interestingly, filters achieve comparable or even better results with respect to the GA-based wrappers, while also being easier and faster to implement. Taken together, our findings suggest that simple, well-established feature selectors in combination with optimized classifiers guarantee good performances, with no need for complicated and computationally demanding methodologies.

Integrating metabolome dynamics and process data to guide cell line selection in biopharmaceutical process development.

The successful development of mammalian cell culture for the production of therapeutic antibodies is a resource-intensive and multistage process which requires the selection of high performing and stable cell lines at different scale-up stages. Accordingly, science-based approaches exploiting biological information, such as metabolomics, can support and accelerate the selection of promising cell lines to progress. In fact, the integration of dynamic biological information with process data can provide valuable insights on the cell physiological changes as a consequence of the cultivation process. This work studies the industrial development of monoclonal antibodies at micro-bioreactor scale (Ambr®15) and aims at accelerating the selection of the better performing cell lines. To that end, we apply a machine learning approach to integrate time-varying process and biological information (i.e., metabolomics), explicitly exploiting their dynamics. Strikingly, cell line performance during the cultivation can be predicted from early process timepoints by exploiting the gradual temporal evolution of metabolic phenotypes. Furthermore, product titer is estimated with good accuracy at late process timepoints, providing insights into its relationship with underlying metabolic mechanisms and enabling the identification of biomarkers to be further investigated. The biological insights obtained through the proposed machine learning approach provide data-driven metabolic understanding allowing early identification of high performing cell lines. Additionally, this analysis offers the opportunity to identify key metabolites which could be used as biomarkers for industrially relevant phenotypes and onward fit into our commercial manufacturing platforms.

Streamlining tablet lubrication design via model-based design of experiments.

In oral solid dosage production through direct compression powder lubrication must be carefully selected to facilitate the manufacturing of tablets without degrading product manufacturability and quality (e.g. dissolution). To do so, several semi-empirical models relating compression performance to process operating conditions have been developed. Among them, we consider an extension of the Kushner and Moore model (Kushner and Moore, 2010, International Journal Pharmaceutics, 399:19) that is useful for the purpose, but requires an extensive experimental campaign for parameters identification. This implies the preparation and compression of multiple powder blends, each one with a different lubrication extent. In turn, this translates into a considerable consumption of Active Pharmaceutical Ingredient (API), and into time-consuming experiments. We tackled this issue by proposing a novel model-based design of experiments (MBDoE) approach, which minimizes the number of optimal blends for model calibration, while obtaining statistically sound parameters estimates and model predictions. Both sequential and parallel MBDoE configurations were compared. Experimental results involving two placebo blends with different lubrication sensitivity showed that this methodology is able to reduce the experimental effort by 60-70% with respect to the standard industrial practice independently of the formulation considered and configuration (i.e. parallel vs. sequential) adopted.

Optimization of the Appearance Quality in CO2 Processed Ready-to-Eat Carrots through Image Analysis.

A high-pressure CO2 process applied to ready-to-eat food products guarantees an increase of both their microbial safety and shelf-life. However, the treatment often produces unwanted changes in the visual appearance of products depending on the adopted process conditions. Accordingly, the alteration of the visual appearance influences consumers' perception and acceptability. This study aims at identifying the optimal treatment conditions in terms of visual appearance by using an artificial vision system. The developed methodology was applied to fresh-cut carrots (Daucus carota) as the test product. The results showed that carrots packaged in 100% CO2 and subsequently treated at 6 MPa and 40 °C for 15 min maintained an appearance similar to the fresh product for up to 7 days of storage at 4 °C. Mild appearance changes were identified at 7 and 14 days of storage in the processed products. Microbiological analysis performed on the optimal treatment condition showed the microbiological stability of the samples up to 14 days of storage at 4 °C. The artificial vision system, successfully applied to the CO2 pasteurization process, can easily be applied to any food process involving changes in the appearance of any food product.

Data analytics on raw material properties to accelerate pharmaceutical drug development.

Manufacturability of active pharmaceutical ingredients (APIs) is often evaluated by an empirical approach during development due to limited material availability. This brings challenges in designing flexible yet robust manufacturing processes under highly accelerated timelines. Hence, good utilisation of a limited material dataset is key to accelerate the delivery of high quality final drug product into the market at minimum cost and maximum process capacity. In this study, we present a data-driven method to investigate a raw materials database where the integration of multivariate analysis and machine learning modelling aids the selection of new incoming materials based on their manufacturability. The procedure was applied to an industrial representative database of thirty-four APIs and seven excipients where eight measurements relevant to flow properties for each of those forty-one materials were collected. The models identified four clusters of materials with different flow properties. These models can serve as a risk assessment tool for new API in early product development phases based on the nearest surrogate material which behave similarly, as well as to identify targeted and material sparring experiments to address key risks during secondary process selection.

Agricultural by-products with bioactive effects: A multivariate approach to evaluate microbial and physicochemical changes in a fresh pork sausage enriched with phenolic compounds from olive vegetation water.

The use of phenolic compounds derived from agricultural by-products could be considered as an eco-friendly strategy for food preservation. In this study a purified phenol extract from olive vegetation water (PEOVW) was explored as a potential bioactive ingredient for meat products using Italian fresh sausage as food model. The research was developed in two steps: first, an in vitro delineation of the extract antimicrobial activities was performed, then, the PEOVW was tested in the food model to investigate the possible application in food manufacturing. The in vitro tests showed that PEOVW clearly inhibits the growth of food-borne pathogens such as Listeria monocytogenes and Staphylococcus aureus. The major part of Gram-positive strains was inhibited at the low concentrations (0.375-3mg/mL). In the production of raw sausages, two concentrates of PEOVW (L1: 0.075% and L2: 0.15%) were used taking into account both organoleptic traits and the bactericidal effects. A multivariate statistical approach allowed the definition of the microbial and physicochemical changes of sausages during the shelf life (14days). In general, the inclusion of the L2 concentration reduced the growth of several microbial targets, especially Staphylococcus spp. and LABs (2log10CFU/g reduction), while the increasing the growth of yeasts was observed. The reduction of microbial growth could be involved in the reduced lipolysis of raw sausages supplemented with PEOVW as highlighted by the lower amount of diacylglycerols. Moisture and aw had a significant effect on the variability of microbiological features, while food matrix (the sausages' environment) can mask the effects of PEOVW on other targets (e.g. Pseudomonas). Moreover, the molecular identification of the main representative taxa collected during the experimentation allowed the evaluation of the effects of phenols on the selection of bacteria. Genetic data suggested a possible strain selection based on storage time and the addition of phenol compounds especially on LABs and Staphylococcus spp. The modulation effects on lipolysis and the reduction of several microbial targets in a naturally contaminated product indicates that PEOVW may be useful as an ingredient in fresh sausages for improving food safety and quality.

Knowledge management in secondary pharmaceutical manufacturing by mining of data historians-A proof-of-concept study.

In this proof-of-concept study, a methodology is proposed to systematically analyze large data historians of secondary pharmaceutical manufacturing systems using data mining techniques. The objective is to develop an approach enabling to automatically retrieve operation-relevant information that can assist the management in the periodic review of a manufactory system. The proposed methodology allows one to automatically perform three tasks: the identification of single batches within the entire data-sequence of the historical dataset, the identification of distinct operating phases within each batch, and the characterization of a batch with respect to an assigned multivariate set of operating characteristics. The approach is tested on a six-month dataset of a commercial-scale granulation/drying system, where several millions of data entries are recorded. The quality of results and the generality of the approach indicate that there is a strong potential for extending the method to even larger historical datasets and to different operations, thus making it an advanced PAT tool that can assist the implementation of continual improvement paradigms within a quality-by-design framework.

Quality-by-Design approach to monitor the operation of a batch bioreactor in an industrial avian vaccine manufacturing process.

Monitoring batch bioreactors is a complex task, due to the fact that several sources of variability can affect a running batch and impact on the final product quality. Additionally, the product quality itself may not be measurable on line, but requires sampling and lab analysis taking several days to be completed. In this study we show that, by using appropriate process analytical technology tools, the operation of an industrial batch bioreactor used in avian vaccine manufacturing can be effectively monitored as the batch progresses. Multivariate statistical models are built from historical databases of batches already completed, and they are used to enable the real time identification of the variability sources, to reliably predict the final product quality, and to improve process understanding, paving the way to a reduction of final product rejections, as well as to a reduction of the product cycle time. It is also shown that the product quality "builds up" mainly during the first half of a batch, suggesting on the one side that reducing the variability during this period is crucial, and on the other side that the batch length can possibly be shortened. Overall, the study demonstrates that, by using a Quality-by-Design approach centered on the appropriate use of mathematical modeling, quality can indeed be built "by design" into the final product, whereas the role of end-point product testing can progressively reduce its importance in product manufacturing.

Vibrio trends in the ecology of the Venice lagoon.

Vibrio is a very diverse genus that is responsible for different human and animal diseases. The accurate identification of Vibrio at the species level is important to assess the risks related to public health and diseases caused by aquatic organisms. The ecology of Vibrio spp., together with their genetic background, represents an important key for species discrimination and evolution. Thus, analyses of population structure and ecology association are necessary for reliable characterization of bacteria and to investigate whether bacterial species are going through adaptation processes. In this study, a population of Vibrionaceae was isolated from shellfish of the Venice lagoon and analyzed in depth to study its structure and distribution in the environment. A multilocus sequence analysis (MLSA) was developed on the basis of four housekeeping genes. Both molecular and biochemical approaches were used for species characterization, and the results were compared to assess the consistency of the two methods. In addition, strain ecology and the association between genetic information and environment were investigated through statistical models. The phylogenetic and population analyses achieved good species clustering, while biochemical identification was demonstrated to be imprecise. In addition, this study provided a fine-scale overview of the distribution of Vibrio spp. in the Venice lagoon, and the results highlighted a preferential association of the species toward specific ecological variables. These findings support the use of MLSA for taxonomic studies and demonstrate the need to consider environmental information to obtain broader and more accurate bacterial characterization.

Latent variable modeling to assist the implementation of Quality-by-Design paradigms in pharmaceutical development and manufacturing: a review.

The introduction of the Quality-by-Design (QbD) initiative and of the Process Analytical Technology (PAT) framework by the Food and Drug Administration has opened the route to the use of systematic and science-based approaches to support pharmaceutical development and manufacturing activities. In this review we discuss the role that latent variable models (LVMs) can play in the practical implementation of QbD paradigms in the pharmaceutical industry, and the potential they may have in assisting the development and manufacturing of new products. The ultimate scope is to provide practitioners with a perspective on the effectiveness of the use of LVMs in any phase of the development of a pharmaceutical product, from its design up to its commercial production. After an overview of the main regulatory paradigms the QbD initiative is founded on, we show how LVMs can be feasibly used to support pharmaceutical development and manufacturing activities while matching the regulatory Agencies' requirements. Three main areas are identified, wherein the use of LVMs can provide significant benefits: (i) process understanding, (ii) product and process design, and (iii) process monitoring and control. For each of them, the main contributions recently appeared in the literature are reviewed. Issues open for further research are also identified.

A correlative study on data from pork carcass and processed meat (Bauernspeck) for automatic estimation of chemical parameters by means of near-infrared spectroscopy.

The use of near-infrared spectroscopy (NIRS) is proposed in this study for the characterization of the quality parameters of a smoked and dry-cured meat product known as Bauernspeck (originally from Northern Italy), as well as of some technological traits of the pork carcass used for its manufacturing. In particular, NIRS is shown to successfully estimate several key quality parameters (including water activity, moisture, dry matter, ash and protein content), suggesting its suitability for real time application in replacement of expensive and time consuming chemical analysis. Furthermore, a correlative approach based on canonical correlation analysis was used to investigate the spectral regions that are mostly correlated to the characteristics of interest. The identification of these regions, which can be linked to the absorbance of the main functional chemical groups, is intended to provide a better understanding of the chemical structure of the substrate under investigation.

General procedure to aid the development of continuous pharmaceutical processes using multivariate statistical modeling - an industrial case study.

Streamlining the manufacturing process has been recognized as a key issue to reduce production costs and improve safety in pharmaceutical manufacturing. Although data available from earlier developmental stages are often sparse and unstructured, they can be very useful to improve the understanding about the process under development. In this paper, a general procedure is proposed for the application of latent variable statistical methods to support the development of new continuous processes in the presence of limited experimental data. The proposed procedure is tested on an industrial case study concerning the development of a continuous line for the manufacturing of paracetamol tablets. The main driving forces acting on the process are identified and ranked according to their importance in explaining the variability in the available data. This improves the understanding about the process by elucidating how different active pharmaceutical ingredient pretreatments, different formulation modes and different settings on the processing units affect the overall operation as well as the properties of the intermediate and final products. The results can be used as a starting point to perform a comprehensive and science-based quality risk assessment that help to define a robust control strategy, possibly enhanced with the integration of a design space for the continuous process at a later stage.

Use of near-infrared spectroscopy for fast fraud detection in seafood: application to the authentication of wild European sea bass (Dicentrarchus labrax).

The possibility of using near-infrared spectroscopy (NIRS) for the authentication of wild European sea bass ( Dicentrarchus labrax ) was investigated in this study. Three different chemometric techniques to process the NIR spectra were developed, and their ability to discriminate between wild and farmed sea bass samples was evaluated. One approach used spectral information to directly build the discrimination model in a latent variable space; the second approach first used wavelets to transform the spectral information and subsequently derived the discrimination model using the transformed spectra; in the third approach a cascaded arrangement was proposed whereby very limited chemical information was first estimated from spectra using a regression model, and this estimated information was then used to build the discrimination model in a latent variable space. All techniques showed that NIRS can be used to reliably discriminate between wild and farmed sea bass, achieving the same classification performance as classification methods that use chemical properties and morphometric traits. However, compared to methods based on chemical analysis, NIRS-based classification methods do not require reagents and are simpler, faster, more economical, and environmentally safer. All proposed techniques indicated that the most predictive spectral regions were those related to the absorbance of groups CH, CH(2), CH(3), and H(2)O, which are related to fat, fatty acids, and water content.