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The general aim of the project SUS&LOW is to increase the sustainability of fresh produce by testing and implementing lowinput agricultural practices (LIP) with positive impact on product quality with the support of nondestructive (ND) tools for realtime quality assessment and for product discrimination. Additionally, new marketing strategies are generated to better support the added value of the products and to satisfy the final consumers' preferences. The SUS&LOW project consists of three work packages (WP) and the adopted methodology used two model crops: rocket salad and tomato. The WP1, focused on the reduction of agricultural inputs, showed that sensorbased fertigation management might improve sustainability of soilless cultivation. Results coming from WP2, aimed to the evaluation of ND techniques, outlined the high potentiality of hyperspectral imaging (HSI) and Fourier transformednear infrared (FTNIR) techniques for the authentication of sustainable growing methods. Moreover, project activities' proved computer vision system (CVS) as an effective tool for evaluating the product quality also through the bag. The WP3, dealing with marketing strategies, indicated a positive approach of consumers compared to LIP products certified through a visual storytelling platform. [ABSTRACT FROM AUTHOR]

Table grapes are characterized by high susceptibility to mold development during postharvest, mostly due to Botrytis cinerea. Microwave application on readytoeat product can represent an alternative to antifungal treatment. With the aim of identifying the maximum energy that can be applied on grape without detrimental effects a Central Composite Design was developed testing the application of 10 combinations of treatment time (seconds) and microwave power (Watt). As a result, energies above 8000 kJ negatively affected the sensorial quality of fresh product, both in the presence and absence of B. cinerea inoculum (106 log CFU g1). The physicochemical parameters did not show significant differences, but two time/power combinations improved sensory quality of table grape, being selected for the subsequent packaging trial: 14 s/100 W and 80 s/100 W. Treatments were applied before or after packaging in polypropylene bags. At the end of storage period, 100 W applied for 80 seconds before packaging led to a better external appearance of the product than the other treatments, maintaining an intermediate level of mesophilic bacterial load and no significant differences in terms of nutritional quality. 80 seconds at 100 Watt combined with packaging can represent a valuable starting point for further experiments. [ABSTRACT FROM AUTHOR]

This study was aimed to investigate the quality at harvest and during storage of organically and conventionally grown 'Italia' grapes, collected from 2 different locations in Southern Italy. Four vineyards were chosen in order to have an organic and a conventional farm in each location. Before harvest, six plants per vineyard were randomly selected and considered as treatment replicate. Three bunches were harvested and labelled from each plant. In laboratory each bunch was weighed and thirty berries per bunch were detached and used for initial determination which included morphological (berry weight and dimension, peel thickness) and physical (berry color and firmness) attributes, maturity indices (respiration rate, soluble solids content and titratable acidity), and nutritional composition (phenol content, antioxidant activity, sugar and organic acid composition, ascorbic acid content). Then, the bunches from each replicate were kept in individual 15L jars at 0°C and connected to a humidified air flow throughout the whole experiment. After 7 and 14 days of storage, respiration rate, weight loss, physical and nutritional attributes were also monitored on 20 berries per bunch. Location and agricultural practices affected to a different extent several grapes quality attributes, both at harvest and during storage. Maturity stage, sugar content and berry color were significantly affected by the location, while antioxidantrelated compounds were significantly higher in organic grapes. Plant production and bunch weight were significantly higher for conventionally grown grapes, which also received the highest evaluation of external appearance, in terms of stalk dehydration and berry general aspect. Differences among conventional and organic grapes were maintained, for each location, during storage at 0°C. Conventional grapes maintained a higher visual quality during storage, resulting after 14 days below the limit of marketability (score 3) but above the edibility limit (score 2); whereas in one location organic grapes were judged not edible. Results showed a higher nutritional value in grapes obtained with the organic farming system although in terms of visual quality, storability and yield, conventional fruit had a better performance. [ABSTRACT FROM AUTHOR]

Wounding makes fresh-cut product more perishable than whole fruit. The effect of wounding intensity on respiration rate and nutritional quality of fresh-cut 'Candonga' strawberries was investigated. Fruit were submitted to six levels of cutting intensity - whole fruit (WHO), 4, 16, 64, and 128 pieces and chopped (CHO) samples. Respiration rate, and the main nutritional parameters were evaluated at the processing day and after 2 days of storage at 5°C. Results showed that wounding intensity significantly influenced respiration rate, ascorbic and dehydroascorbic acids, total phenolic content, and antioxidant capacity. Respiration rate increased with wounding intensity up to the level of 64 pieces (10.01 μg kg-1 s-1) compared to WHO (5.5 μg kg-1 s-1) and then decreased in the CHO samples (2.81 μg kg-1 s-1). At Day 2, the stress caused by the high intensity of cutting (64 pieces and CHO) induced a higher degradation of ascorbic acid, phenolic compounds, and antioxidant capacity. Stress-related changes decrease when the wounding damage was so high that it completely compromises the functionality of the cells (from 64 pieces up). These results should be considered for processing and packaging optimization of minimally processed strawberries-based products. [ABSTRACT FROM AUTHOR]

'Catanese' artichoke quarters were packaged in active modified atmosphere (5% O2+10% CO2) in four different materials or in air in macro-perforated bags used as control (CTRL), and stored at 4°C. Materials used for modified atmosphere packaging (MAP) were: polylactic acid (PLA), polylactid acid with one line of micro-perforation (PLA MF1), polypropilene with two lines of micro-perforations (PP MF2), and polypropylene + polyamide with two lines of micro-perforations (PP+PA MF2). Initially and after 2, 4, and 9 days, overall artichoke appearance, color and weight loss were monitored. O2 and CO2 concentrations within the packages were detected initially and after 1, 2, 17, 24.5, 41.5, 49.5, 120 and 216 h (end of the experiment). Also, at the last sampling date ethanol and acetaldehyde accumulations in artichoke tissue were measured. All the micro-perforated films maintained gas levels within the range of O2>3% and CO2<15%, defined as "safe", with a positive effect on quality: all samples remained above the limit of marketability until the end of the experiment, without significant differences among them, but showed a slight better overall appearance and, accordingly, a better retention of color parameters when compared with CTRL samples. Complete anaerobic condition (16% CO2 and 0% O2) developed in PLA bags where blackening of cut bracts and receptacle was observed, while black spots appeared on outer bracts, causing drastic quality reduction; samples fell below the limit of marketability after just 2 days. Also a significant accumulation of ethanol and acetaldehyde was found in these samples. Optimizing MAP made it possible to maintain the desired gas condition, with positive effects on quality of the produce in absence of any stabilizing treatment, for 9 days. [ABSTRACT FROM AUTHOR]

A high time-resolved monitoring campaign of bulk deposition of PAHs and metals was conducted near the industrial area and at an urban background site in province of Taranto (Italy) in order to evaluate the impact of the biggest European steel plant. The deposition fluxes of the sum of detected PAHs at the industrial area ranged from 92 to 2432 ng m-2 d-1. In particular the deposition fluxesofBaP, BaA, and BkFwere, on average, 10, 14, and 8 times higher than those detected at the urban back ground site, respectively. The same finding was for metals. The deposition fluxes of Ni (19.8 µgm-2 d-1) andAs (2.2 µgm-2 d-1) at the industrial site were about 5 times higher than those at the urban background site, while the deposition fluxes of Fe (57 mg m-2 d-1) and Mn (1.02 mg m-2 d-1) about 31 times higher. Precipitation and wind speed played an important role in PAH deposition fluxes. Fe and Mn fluxes at the industrial site resulted high when wind direction favored the transport of air masses from the steel plant to the receptor site. The impact of the industrial area was also confirmed by IP/(IP + BgP), IP/BgP, and BaP/BgP diagnostic ratios. [ABSTRACT FROM AUTHOR]

Abstract: An assessment of the fugitive emission impact on ambient air PM, PAHs and metal concentrations was performed in a residential area near the biggest European steel plant. A careful experimental design was developed to characterize fugitive emissions produced by the integrated steel plant. A PM10 and PM2.5 monitoring campaign was conducted at three sampling sites around the steel plant, in order to perform a triangulation in the area surrounding the investigated site and evaluate its impact based on wind direction. Data analysis showed that the transport of air mass, from the steelworks to one of the receptor sites, resulted in ambient air concentrations of Fe, Mn, Zn and PAHs higher than those observed in the other two sites. Principal component analysis allowed the identification of four emission sources: coke ovens stack, mineral park, a crustal source and vanadium source. The first two sources were characterized by high concentrations of PAHs and metals and related to the steelworks, while the vanadium source was probably associated with maritime traffic in the port area. This preliminary monitoring approach proved effective in identifying the fugitive emission contribution of the steel plant to the surrounding air quality. [Copyright &y& Elsevier]

The quality of fresh-cut fruit and vegetable products includes a combination of attributes, such as appearance, texture, and flavor, as well as nutritional and safety aspects that determine their value to the consumer. Nutritionally, fruit and vegetables represent a good source of vitamins, minerals, and dietary fiber, and fresh-cut produce satisfies consumer demand for freshly prepared, convenient, healthy food. However, fresh-cut produce deteriorates faster than corresponding intact produce, as a result of damage caused by minimal processing, which accelerates many physiological changes that lead to a reduction in produce quality and shelf-life. The symptoms of produce deterioration include discoloration, increased oxidative browning at cut surfaces, flaccidity as a result of loss of water, and decreased nutritional value. Damaged plant tissues also represent a better substrate for growth of microorganisms, including spoilage microorganisms and foodborne pathogens. The risk of pathogen contamination and growth is one of the main safety concerns associated with fresh-cut produce, as highlighted by the increasing number of produce-linked foodborne outbreaks in recent years. The pathogens of major concern in fresh-cut produce are Listeria monocytogenes, pathogenic Escherichia coli mainly O157:H7, and Salmonella spp. This article describes the quality of fresh-cut produce, factors affecting quality, and various techniques for evaluating quality. In addition, the microbiological safety of fresh-cut produce and factors affecting pathogen survival and growth on fresh-cut produce are discussed in detail. [ABSTRACT FROM AUTHOR]

Summary Although there is little information from primary or secondary prevention trials on cholesterol-lowering medication in diabetic patients, the reduction of elevated cholesterol is widely recommended for this group. The American Diabetes Association (ADA) recommends drug therapy in diabetic patients if low density lipoprotein (LDL)-cholesterol remains at > 130 mg/dl, or > 100 mg/dl in patients with macroangiopathy, after dietary intervention. When cholesterol-lowering medication is indicated, the choice of the drug must take into account the other lipid abnormalities that are often present and the need to maintain optimal glycaemic control. In the present study we compared the efficacy and safety of the novel HMG-CoA reductase inhibitor atorvastatin at the dose of 10 mg/day with simvastatin , lovastatin and pravastatin at doses of 10, 20 and 20 mg/day, respectively, and placebo, in type 2 diabetic patients with moderate elevation of LDL-cholesterol with or without elevation of triglycerides. All the quoted agents are enzyme inhibitors effective in lowering LDL-cholesterol in humans. The efficacy endpoints were the mean per cent changes in plasma LDL-cholesterol (primary), total cholesterol, triglycerides, and high-density lipoprotein (HDL)-cholesterol concentrations from baseline to the end of treatment (24 weeks). Atorvastatin at a dose of 10 mg/day produced: (1) a significant reduction in LDL-cholesterol (- 37%) in comparison with equivalent doses of simvastatin (- 26%), pravastatin (- 23%), lovastatin (- 21%), and placebo (- 1%); (2) HDL-cholesterol increases (7.4%) comparable to or greater than those obtained with simvastatin (7.1%), pravastatin (3.2%), lovastatin (7.21%), and placebo (- 0.5%); (3) a significantly greater reduction in total cholesterol (- 29%) than that obtained with simvastatin (- 21%), pravastain (- 16%), lovastatin (- 18%), and placebo (1%); and (4) a significantly greater reduction in triglycerides than that obtained with... [ABSTRACT FROM AUTHOR]

Vancomycin instilled in an Ommaya reservoir was used to treat a reservoir-associated infection. Vancomycin concentrations in cerebrospinal fluid (CSF) were measured, and derivation of pharmacokinetic parameters allowed tailoring of dosing. First-order kinetics were observed. The calculated half-life of 3.52 h was less than reported by others, and the apparent volume of distribution (60 ml) was less than anticipated. The elimination constant was 0.197 h−1, Empiric dosing based on schedules suggested in the literature would have led to high peak and low mean concentrations of intrareservoir vancomycin. Patients with reservoir-associated infections have a variety of pathophysiologic conditions that can result in alteration of normal CSF dynamics. Pharmacokinetic analysis is useful to individualize dosing and to optimize therapy with intrareservoir vancomycin. [ABSTRACT FROM PUBLISHER]

Studies on human parathyroids are generally limited to hyperfunctioning glands owing to the difficulty in obtaining normal human tissue. We therefore obtained non-human primate (NHP) parathyroids to provide a suitable alternative for sequencing that would bear a close semblance to human organs. Single-cell RNA expression analysis of parathyroids from four healthy adult M. mulatta reveals a continuous trajectory of epithelial cell states. Pseudotime analysis based on transcriptomic signatures suggests a progression from GCM2 hi progenitors to mature parathyroid hormone ( PTH )-expressing epithelial cells with increasing core mitochondrial transcript abundance along pseudotime. We sequenced, as a comparator, four histologically characterized hyperfunctioning human parathyroids with varying oxyphil and chief cell abundance and leveraged advanced computational techniques to highlight similarities and differences from non-human primate parathyroid expression dynamics. Predicted cell-cell communication analysis reveals abundant endothelial cell interactions in the parathyroid cell microenvironment in both human and NHP parathyroid glands. We show abundant RARRES2 transcripts in both human adenoma and normal primate parathyroid cells and use coimmunostaining to reveal high levels of RARRES2 protein (also known as chemerin) in PTH-expressing cells, which could indicate that RARRES2 plays an unrecognized role in parathyroid endocrine function. The data obtained are the first single-cell RNA transcriptome to characterize nondiseased parathyroid cell signatures and to show a transcriptomic progression of cell states within normal parathyroid glands, which can be used to better understand parathyroid cell biology., (© 2024 Venkat et al.; Published by Cold Spring Harbor Laboratory Press.)

Exciting advances in technologies to measure biological systems are currently at the forefront of research. The ability to gather data along an increasing number of omic dimensions has created a need for tools to analyze all of this information together, rather than siloing each technology into separate analysis pipelines. To advance this goal, we introduce a framework called the single-cell multi-modal generative adversarial network (scMMGAN) that integrates data from multiple modalities into a unified representation in the ambient data space for downstream analysis using a combination of adversarial learning and data geometry techniques. The framework's key improvement is an additional diffusion geometry loss with a new kernel that constrains the otherwise over-parameterized GAN. We demonstrate scMMGAN's ability to produce more meaningful alignments than alternative methods on a wide variety of data modalities and that its output can be used to draw conclusions from real-world biological experimental data., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

Often when biological entities are measured in multiple ways, there are distinct categories of information: some information is easy-to-obtain information (EI) and can be gathered on virtually every subject of interest, while other information is hard-to-obtain information (HI) and can only be gathered on some. We propose building a model to make probabilistic predictions of HI using EI. Our feature mapping GAN (FMGAN), based on the conditional GAN framework, uses an embedding network to process conditions as part of the conditional GAN training to create manifold structure when it is not readily present in the conditions. We experiment on generating RNA sequencing of cell lines perturbed with a drug conditioned on the drug's chemical structure and generating FACS data from clinical monitoring variables on a cohort of COVID-19 patients, effectively describing their immune response in great detail., Competing Interests: The authors declare no competing interests., (© 2021 The Authors.)

While generative models such as GANs have been successful at mapping from noise to specific distributions of data, or more generally from one distribution of data to another, they cannot isolate the transformation that is occurring and apply it to a new distribution not seen in training. Thus, they memorize the domain of the transformation, and cannot generalize the transformation out of sample . To address this, we propose a new neural network called a Neuron Transformation Network (NTNet) that isolates the signal representing the transformation itself from the other signals representing internal distribution variation. This signal can then be removed from a new dataset distributed differently from the original one trained on. We demonstrate the effectiveness of our NTNet on more than a dozen synthetic and biomedical single-cell RNA sequencing datasets, where the NTNet is able to learn the data transformation performed by genetic and drug perturbations on one sample of cells and successfully apply it to another sample of cells to predict treatment outcome.

While neural networks are powerful approximators used to classify or embed data into lower dimensional spaces, they are often regarded as black boxes with uninterpretable features. Here we propose Graph Spectral Regularization for making hidden layers more interpretable without significantly impacting performance on the primary task. Taking inspiration from spatial organization and localization of neuron activations in biological networks, we use a graph Laplacian penalty to structure the activations within a layer. This penalty encourages activations to be smooth either on a predetermined graph or on a feature-space graph learned from the data via co-activations of a hidden layer of the neural network. We show numerous uses for this additional structure including cluster indication and visualization in biological and image data sets.

The genus Flavivirus contains many mosquito-borne human pathogens of global epidemiological importance such as dengue virus, West Nile virus, and Zika virus, which has recently emerged at epidemic levels. Infections with these viruses result in divergent clinical outcomes ranging from asymptomatic to fatal. Myriad factors influence infection severity including exposure, immune status and pathogen/host genetics. Furthermore, pre-existing infection may skew immune pathways or divert immune resources. We profiled immune cells from dengue virus-infected individuals by multiparameter mass cytometry (CyTOF) to define functional status. Elevations in IFNβ were noted in acute patients across the majority of cell types and were statistically elevated in 31 of 36 cell subsets. We quantified response to in vitro (re)infection with dengue or Zika viruses and detected a striking pattern of upregulation of responses to Zika infection by innate cell types which was not noted in response to dengue virus. Significance was discovered by statistical analysis as well as a neural network-based clustering approach which identified unusual cell subsets overlooked by conventional manual gating. Of public health importance, patient cells showed significant enrichment of innate cell responses to Zika virus indicating an intact and robust anti-Zika response despite the concurrent dengue infection., Competing Interests: The authors have declared that no competing interests exist.

It is currently challenging to analyze single-cell data consisting of many cells and samples, and to address variations arising from batch effects and different sample preparations. For this purpose, we present SAUCIE, a deep neural network that combines parallelization and scalability offered by neural networks, with the deep representation of data that can be learned by them to perform many single-cell data analysis tasks. Our regularizations (penalties) render features learned in hidden layers of the neural network interpretable. On large, multi-patient datasets, SAUCIE's various hidden layers contain denoised and batch-corrected data, a low-dimensional visualization and unsupervised clustering, as well as other information that can be used to explore the data. We analyze a 180-sample dataset consisting of 11 million T cells from dengue patients in India, measured with mass cytometry. SAUCIE can batch correct and identify cluster-based signatures of acute dengue infection and create a patient manifold, stratifying immune response to dengue.

Type 1 diabetes (T1D) is most likely caused by killing of β cells by autoreactive CD8 + T cells. Methods to isolate and identify these cells are limited by their low frequency in the peripheral blood. We analyzed CD8 + T cells, reactive with diabetes Ags, with T cell libraries and further characterized their phenotype by CyTOF using class I MHC tetramers. In the libraries, the frequency of islet Ag-specific CD45RO + IFN-γ + CD8 + T cells was higher in patients with T1D compared with healthy control subjects. Ag-specific cells from the libraries of patients with T1D were reactive with ZnT8 186-194 , whereas those from healthy control recognized ZnT8 186-194 and other Ags. ZnT8 186-194 -reactive CD8 + cells expressed an activation phenotype in T1D patients. We found TCR sequences that were used in multiple library wells from patients with T1D, but these sequences were private and not shared between individuals. These sequences could identify the Ag-specific T cells on a repeated draw, ex vivo in the IFN-γ + CD8 + T cell subset. We conclude that CD8 + T cell libraries can identify Ag-specific T cells in patients with T1D. The T cell clonotypes can be tracked in vivo with identification of the TCR gene sequences., (Copyright © 2018 by The American Association of Immunologists, Inc.)

An annual monitoring campaign of VOCs, consisting of twelve sampling periods, was carried out from June 2008 to June 2009 in Modugno, a city located in the Apulia region (Southern Italy), in order to assess the urban air quality, identify the main emission sources, and quantify the cancer and no-cancer risk attributable to inhalation exposures. Monitoring, carried out by using the Radiello diffusive samplers, was conducted in eleven sampling sites throughout the city taking into account the traffic density and the architecture of the city. From the study of the data, it was found that, among all considered VOCs, benzene, toluene, ethylbenzene, and xylenes (BTEX) are the pollutants at higher concentration. The analysis of VOC concentrations, the study of the topography of the city, and the use of different diagnostic ratios between the BTEX species showed that the vehicular traffic emissions were the predominant source of VOCs in the urban area of Modugno. Despite that the annual concentration of benzene is lower than the regulatory limit, the estimation of cancer risk showed that the global lifetime cancer risk attributed to the investigated VOC exposure was not negligible and therefore should be taken into account in future regulatory approaches.

The present work studied how much the meteorological parameters and the emission sources can influence the particulate polycyclic aromatic hydrocarbons (Invalid Journal Information PAHs) concentrations in two areas located in Southern Italy (Bari and Taranto). It was found that when the vehicular traffic is the main source of PAHs, there is a negative correlation between ambient temperature, wind speed and PAHs concentration (Bari). This is because these parameters are generally correlated with the dispersion capacity of the atmosphere. In the presence of a large industrial area, the wind direction becomes an important parameter able to determinate large changes in PAHs concentrations. This happened in Taranto where PAHs concentrations are exceptionally high. During the study the seasonal trend of particulate PAHs and PM10 was compared. PM10 did not show a significant seasonal cycle during the year because it is conditioned from a high regional aerosol background, especially during the summertime. On the contrary, particulate PAHs exerted distinct seasonal variation with higher concentrations in the winter and lower concentration during other months of the year. This evidence suggested that PAHs concentrations can be considered a more reliable index for air-quality assessment. In order to identify an index that considers the contributions of other particulate PAHs, it is necessary to calculate the carcinogenic potency of total PAHs (i.e., total BaPeq) obtained by the sum of the benzo[a]pyrene equivalent concentration (BaPeq) for each PAH.

Objective: To estimate the impact of alcohol consumption on the incidence of mild cognitive impairment and its progression to dementia., Methods: We evaluated the incidence of mild cognitive impairment in 1,445 non-cognitively impaired individuals and its progression to dementia in 121 patients with mild cognitive impairment, aged 65 to 84 years, participating in the Italian Longitudinal Study on Aging, with a 3.5-year follow-up. The level of alcohol consumption was ascertained in the year before the survey. Dementia and mild cognitive impairment were classified using current clinical criteria., Results: Patients with mild cognitive impairment who were moderate drinkers, i.e., those who consumed less than 1 drink/day (approximately 15 g of alcohol), had a lower rate of progression to dementia than abstainers (hazard ratio [HR] 0.15; 95% CI 0.03 to 0.78). Furthermore, moderate drinkers with mild cognitive impairment who consumed less than 1 drink/day of wine showed a significantly lower rate of progression to dementia than abstainers (HR 0.15; 95% CI 0.03 to 0.77). Finally, there was no significant association between higher levels of drinking (> or =1 drink/day) and rate of progression to dementia in patients with mild cognitive impairment vs abstainers. No significant associations were found between any levels of drinking and the incidence of mild cognitive impairment in non-cognitively impaired individuals vs abstainers., Conclusions: In patients with mild cognitive impairment, up to 1 drink/day of alcohol or wine may decrease the rate of progression to dementia.

In the last decade, it has become more apparent the important role genes play in the development of late-onset Alzheimer's disease (AD). Great efforts, involving human genome scans and candidate gene studies, have been given towards identifying susceptibility genes for AD. A number of regions on different chromosomes have been reported to demonstrate linkage for AD. Of these, findings on chromosome 12 are some of the most compelling. Worldwide genetic association studies pre-dating and subsequent to recent linkage studies have identified and focused upon a number of genes that map to the areas of reported linkage on chromosome 12, however, analyses of those genes studied to date, on the whole, remain inconclusive and ambiguous. This paper reviews studies that have provided evidence of linkage for AD on chromosome 12 and in turn discusses the work conducted to date on candidate genes that have been identified and map to the chromosome 12 regions of interest.