Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational and Structural Biotechnology Journal

A principal challenge in computational modeling of macromolecules is the vast conformational space that arises out of large numbers of atomic degrees of freedom. Recently, growing interest in building predictive models of complexes mediated by Proteolysis Targeting Chimeras (PROTACs) has led to the application of state-of-the-art computational techniques to tackle this problem. However, repurposing existing tools to carry out protein-protein docking and linker conformer generation independently results in extensive sampling of structures incompatible with PROTAC-mediated complex formation. Here we show that it is possible to restrict the search to the space of protein-protein conformations that can be bridged by a PROTAC molecule with a given linker composition by using a cyclic coordinate descent algorithm to position PROTACs into complex-bound configurations. We use this methodology to construct potential energy and solvation energy landscapes of PROTAC-mediated interactions. Our results suggest that desolvation of amino acids at interfaces could play a dominant role in PROTAC-mediated complex formation. © 2023 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative-commons.org/licenses/by-nc-nd/4.0/).
Impact of charge patches on tumor disposition and biodistribution of therapeutic antibodies

This study explores the impact of antibody surface charge on tissue distribution into various tissues including tumor. Tumor-bearing mice were dosed intravenously with a mixture comprising three antibodies engineered to carry negative charge patches, a balanced charge distribution, or positive patches, respectively (cassette dosing). Tissue levels were analyzed with a specific LC-MS/MS method. In addition, the antibody mix was administered to non-tumor bearing mice. Muscle and skin interstitial fluid were obtained by centrifugation and analyzed by LC-MS/MS. An in vitro endothelium model was explored for its feasibility to mimic the observed distribution differences. A balanced charge distribution was optimal in terms of total tumor exposure, while in other tissues, negatively charged and balanced charged antibodies gave similar results. In contrast, positive charge patches generally resulted in increased serum clearance but markedly enhanced tumor and organ uptake, leading to higher tissue-to-serum ratios. The uptake and availability in the interstitial space were confirmed by specific assessment of antibody levels in the interstitial fluid of the muscle and skin, with similar charge impact as in total tissue. The in vitro model was able to differentiate the transport propensity of this series of antibody variants. In summary, our results show the differential effects of charge patches on an antibody surface on biodistribution and tumor uptake. These insights may help in the design of molecules with biodistribution properties tailored to their purpose, and an optimized safety profile.
Foliar Application of Copper Nanoparticles Increases the Fruit Quality and the Content of Bioactive Compounds in Tomatoes

: Nanotechnology is a potential and emerging ﬁeld with multiple applications in different areas of study. The beneﬁcial effects of the use of nanoparticles in agriculture have already been proven. The objective of this research was to determine if the foliar application of Cu nanoparticles (NPs) could increase the content of the bioactive compounds in tomato fruits. Our study considered four treatments with different concentrations of Cu nanoparticles (50, 125, 250, 500 mg L − 1 , diameter 50 nm) applied twice during the development of the culture. The effects on the fruit quality and the contents of the antioxidant compounds were determined. The application of the Cu nanoparticles induced the production of fruits with greater ﬁrmness. Vitamin C, lycopene, and the ABTS antioxidant capacity increased compared to the Control. In addition, a decrease in the ascorbate peroxidase (APX) and glutathione peroxidase (GPX) enzymatic activity was observed, while the superoxide dismutase (SOD) and catalase (CAT) enzymes showed a signiﬁcant increase. The application of Cu NPs induced a greater accumulation of bioactive compounds in tomato fruits.
Fashion Retail Recommendation System by Multiple Clustering

— Fashion retail has a large popularity and relevance, allowing customers to buy anytime finding the best offers and providing nice experiences in the shops. Consequently, Customer Relationship Management solutions have been enhanced by Information and Communication Technologies to better understand the behaviour and requirements of customers, engaging and influencing them to improve their buying experience, as well as increasing the retailers’ profitability. Current solutions on marketing provide a too general approach, based on most popular or most purchased items, losing the focus on the customer centricity. In this paper, a recommendation system for fashion retail shops is proposed, based on a multi clustering approach of items and users’ profiles in online and on physical stores. The proposed solution relies on association rules mining techniques, allowing to predict the purchase behavior of newly acquired customers, thus solving the cold start problems which is typical of current state of the art systems. The presented work has been developed in the context of the Feedback project founded by Regione Toscana, and it has been conducted on real retail company Tessilform, Patrizia Pepe mark. The recommendation system has been validated in store, as well as online.
SENECA: An Attention Support Tool for Context-related Content Learning

In this work, we proposed a tool named SENECA that aims to help the students who follow remote lessons to maintain/capture attention, allowing them to focus on learning led by the context. Among the disadvantages of distance education, especially for subjects who lack awareness, the greatest distractions at home are counted. These distractions cause a movement of the student’s attention from the current lesson to disturbing events. For this reason, there is a need to experiment with new solutions also linked to Information Technology (IT) to improve the focused learning during distance education. Our tool’s technical idea is to create a real-time summary of the topic treated by the teacher. The system captures the text every ﬁve minutes, generates outlines, and scratches them and browses them to eliminate repetitive portions after each survey. On the general generated summary, Natural Language Processing techniques are applied to extract categories and keywords. The latter will show the highlights of the speech.
Preparation of hollow mesoporous silica nanospheres: controllable template synthesis and their application in drug delivery

Hollow mesoporous silica nanospheres were prepared using different types of templates such as iron oxide nanoparticles (magnetite and hematite) and polymer nanospheres (polystyrene and resorcinol formaldehyde resin). The process involves a first step of coating silica on templates along with surfactants and then removal of both templates and surfactants to produce hollow mesoporous silica nanospheres in the second step. TEM, XRD, FTIR, TGA, and N2-adsorption–desorption analysis were used to characterize the samples and indicated the hollow and mesoporous structure of silica nanospheres. Ibuprofen as a drug model was used to investigate the drug adsorption behavior of the silica nanospheres which also showed sustained release properties.
Mineral Element Stocks in the Yedoma Domain: A Novel Method Applied to Ice-Rich Permafrost Regions

With permafrost thaw, significant amounts of organic carbon (OC) previously stored in frozen deposits are unlocked and become potentially available for microbial mineralization. This is particularly the case in ice-rich regions such as the Yedoma domain. Excess ground ice degradation exposes deep sediments and their OC stocks, but also mineral elements, to biogeochemical processes. Interactions of mineral elements and OC play a crucial role for OC stabilization and the fate of OC upon thaw, and thus regulate carbon dioxide and methane emissions. In addition, some mineral elements are limiting nutrients for plant growth or microbial metabolic activity. A large ongoing effort is to quantify OC stocks and their lability in permafrost regions, but the influence of mineral elements on the fate of OC or on biogeochemical nutrient cycles has received less attention and there is an overall lack of mineral element content analyses for permafrost sediments. Here, we combine portable X-ray fluorescence (pXRF) with a bootstrapping technique to provide i) the first large-scale Yedoma domain Mineral Concentrations Assessment (YMCA) dataset, and ii) estimates of mineral element stocks in never thawed (since deposition) ice-rich Yedoma permafrost and previously thawed and partly refrozen Alas deposits. The pXRF method for mineral element quantification is non-destructive and offers a complement to the classical dissolution and measurement by optical emission spectrometry (ICP-OES) in solution. Using this method, mineral element concentrations (Si, Al, Fe, Ca, K, Ti, Mn, Zn, Sr and Zr) were assessed on 1,292 sediment samples from the Yedoma domain with lower analytical effort and lower costs relative to the ICP-OES method. The pXRF measured concentrations were calibrated using alkaline fusion and ICP-OES measurements on a subset of 144 samples (R 2 from 0.725 to 0.996). The results highlight that i) the mineral element stock in sediments of the Yedoma domain (1,387,000 km2) is higher for Si, followed by Al, Fe, K, Ca, Ti, Mn, Zr, Sr, and Zn, and that ii) the stock in Al and Fe (598 ± 213 and 288 ± 104 Gt) is in the same order of magnitude as the OC stock (327–466 Gt).
The Role of Exosomal miRNAs in Glioma: Biological Function and Clinical Application

Gliomas are complex and heterogeneous central nervous system tumors with poor prognosis. Despite the increasing development of aggressive combination therapies, the prognosis of glioma is generally unsatisfactory. Exosomal microRNA (miRNA) has been successfully used in other diseases as a reliable biomarker and even therapeutic target. Recent studies show that exosomal miRNA plays an important role in glioma occurrence, development, invasion, metastasis, and treatment resistance. However, the association of exosomal miRNA between glioma has not been systemically characterized. This will provide a theoretical basis for us to further explore the relationship between exosomal miRNAs and glioma and also has a positive clinical significance in the innovative diagnosis and treatment of glioma.
Recyclable Functional Magnetic Nanoparticles for Fast Demulsification of Waste Metalworking Emulsions Driven by Electrostatic Interactions

Complex multiphase waste metalworking emulsions, which contain large amounts of surfactants and mineral oil, are difficult to treat efficiently by traditional molecular demulsifiers. We synthesized one type of functionalized magnetic nanoparticles grafted with amino groups (M@NH2) to treat waste metalworking emulsions from different mechanical processing factories and investigated the demulsification mechanism. The M@NH2 showed an excellent demulsification performance, achieving 85–97% chemical oxygen demand (COD) removal for most of the waste metalworking emulsions. The results indicated the advantage of the three-step demulsification process (adsorption of M@NH2 on droplets, droplet coalescence, and the magnetic transfer of droplets in the magnetic field) over traditional two-step demulsification (adsorption of MNPs on droplets and the transfer of droplets in the magnetic field). In addition, electrostatic interactions between M@NH2 and surfactants were confirmed as the driving force of demulsification.
Association of ABCG2 rs2231142 Allele and BMI With Hyperuricemia in an East Asian Population

Objectives: Genetic variants and obesity are risk factors for hyperuricemia (HUA). Recent genome-wide association studies have identified ABCG2 rs2231142 as one of the most prominent genetic variants for HUA in an East Asian population. Nevertheless, no large-scale studies have demonstrated any interactive effects between this variant and obesity on serum urate level in Asians. This study aimed to determine the interaction of ABCG2 rs2231142 variant and body mass index (BMI) and its effect on risk of HUA in an East Asian population. Methods: The study was conducted using the Taiwan Biobank database, a population-based biomedical research database of patients with Taiwanese Han Chinese ancestry aged 30–70years between September 2014 and May 2017. Detailed physical information on participants were collected by questionnaires and genotyping using Affymetrix TWB 650K SNP chip. The primary outcome was HUA, defined as a serum uric acid level>7.0mg/dl. Odds ratio (OR) of HUA was analyzed using logistic regression models and the effects of interaction between ABCG2 rs2231142 variants and BMI on serum uric acid level were explored. Results: We identified 25,245 subjects, 4,228 (16.75%) of whom had HUA. The prevalence of HUA was 30% in men and 3.8% in women. The risk of HUA was significantly associated with ABCG2 rs2231142 risk T allele, with more HUA in TT genotype (OR: 2.40, 95% CI: 2.11–2.72, p<0.001) and TG genotype (OR: 1.64, 95% CI: 1.51–1.78, p<0.001) in men, and TT genotype (OR: 2.42, 95% CI: 1.83–3.20, p<0.001) and TG genotype (OR: 1.82, 95% CI: 1.46–2.23, p<0.001) in women, compared with their counterparts. Moreover, we found a strong genetic-environmental interaction associated with the risk of HUA. There was increased risk of HUA by the interaction of ABCG2 rs2231142 variant and BMI for TT genotype (OR: 7.42, 95% CI: 2.54–21.7, p<0.001) and TG genotype (OR: 4.25, 95% CI: 2.13–8.47, p<0.001) in men compared with the GG genotype in men, and for TT genotype (OR: 25.43, 95% CI: 3.75–172.41, p<0.001) and TG genotype (OR: 3.05, 95% CI: 0.79–11.71, p=0.011) in women compared with the GG genotype in women. Conclusion: The risk of HUA was markedly increased by the interaction of ABCG2 rs2231142 variant and BMI, both in men and in women. Body weight control and reduction in BMI are recommended in high-risk patients with the ABCG2 rs2231142 risk T allele.
Blocking miR530 Improves Rice Resistance, Yield, and Maturity

MicroRNAs fine-tune plant growth and resistance against multiple biotic and abiotic stresses. The trade-off between biomass and resistance can penalize crop yield. In this study, we have shown that rice miR530 regulates blast disease resistance, yield, and growth period. While the overexpression of miR530 results in compromised blast disease resistance, reduced grain yield, and late maturity, blocking miR530 using a target mimic (MIM530) leads to enhanced resistance, increased grain yield, and early maturity. Further study revealed that the accumulation of miR530 was decreased in both leaves and panicles along with the increase of age. Such expression patterns were accordant with the enhanced resistance from seedlings to adult plants, and the grain development from panicle formation to fully-filled seeds. Divergence analysis of miR530 precursor with upstream 1,000-bp promoter sequence in 11 rice species revealed that miR530 was diverse in Oryza sativa japonica and O. sativa indica group, which was consistent with the different accumulation of miR530 in japonica accessions and indica accessions. Altogether, our results indicate that miR530 coordinates rice resistance, yield, and maturity, thus providing a potential regulatory module for breeding programs aiming to improve yield and disease resistance.
Harnessing Inflammation Resolution in Arthritis: Current Understanding of Specialized Pro-resolving Lipid Mediators’ Contribution to Arthritis Physiopathology and Future Perspectives

The concept behind the resolution of inflammation has changed in the past decades from a passive to an active process, which reflects in novel avenues to understand and control inflammation-driven diseases. The time-dependent and active process of resolution phase is orchestrated by the endogenous biosynthesis of specialized pro-resolving lipid mediators (SPMs). Inflammation and its resolution are two forces in rheumatic diseases that affect millions of people worldwide with pain as the most common experienced symptom. The pathophysiological role of SPMs in arthritis has been demonstrated in pre-clinical and clinical studies (no clinical trials yet), which highlight their active orchestration of disease control. The endogenous roles of SPMs also give rise to the opportunity of envisaging these molecules as novel candidates to improve the life quality of rhematic diseases patients. Herein, we discuss the current understanding of SPMs endogenous roles in arthritis as pro-resolutive, protective, and immunoresolvent lipids.
The Burden of Respiratory Viruses and Their Prevalence in Different Geographical Regions of India: 1970–2020

As per the 2019 report of the National Health Portal of India, 41,996,260 cases and 3,740 deaths from respiratory infections were recorded across India in 2018. India contributes to 18% of the global population, with severe acute respiratory infection (SARI) as one of the prominent causes of mortality in children >5 years of age. Measures in terms of the diagnosis and surveillance of respiratory infections are taken up globally to discover their circulating types, detect outbreaks, and estimate the disease burden. Similarly, the purpose of this review was to determine the prevalence of respiratory infections in various regions of India through published reports. Understanding the pattern and prevalence of various viral entities responsible for infections and outbreaks can help in designing better strategies to combat the problem. The associated pathogens comprise respiratory syncytial virus (RSV), rhinovirus, influenza virus, parainfluenza virus, adenovirus, etc. Identification of these respiratory viruses was not given high priority until now, but the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has sensitized our system to be alert about the burden of existing infections and to have proper checks for emerging ones. Most of the studies reported to date have worked on the influenza virus as a priority. However, the data describing the prevalence of other respiratory viruses with their seasonal pattern have significant epidemiological value. A comprehensive literature search was done to gather data from all geographical regions of India comprising all states of India from 1970 to 2020. The same has been compared with the global scenario and is being presented here.
Ecoengineering Solutions for the Impairment of Spreading and Growth of Invasive Spartina patens in Mediterranean Salt Marshes

The invasion of natural communities by non-indigenous species represents one of the most serious threats to biodiversity. Understanding the ecophysiology of invasive species can provide insights into potential physiological handicaps relative to native species. By doing so, we can leverage the development of ecoengineering solutions for the removal of non-indigenous species, preferably using non-chemical methods. Spartina patens is a known invasive species of cordgrass aggressively proliferating in Mediterranean salt marshes, producing impenetrable monospecific stands. As its occurrence is delimited by the upper high tide water level, we hypothesized that S. patens is intolerant to waterlogging. Therefore, we developed a field experiment where strands of S. patens were kept waterlogged over the entire tidal cycle for 30 days. At the end of the experimental period, plants in the trial plots exhibited severe stress symptoms at different physiological levels compared with control plots (no intervention). At the photobiological level, intervened plants exhibited lower efficiency in producing chemical energy from light, whilst at the biochemical level waterlogging impaired the antioxidant system and increased lipid peroxidation products. Furthermore, the application of chlorophyll a pulse amplitude modulated (PAM) fluorometry, a non-invasive technique, allowed us to evaluate the effectiveness of the implemented measures, being the tool that provided the best separation between the control and intervened population. Considering the physiological traits observed here, ecoengineering solutions based on increased waterlogging of S. patens stands, can be a low-cost and efficient measure to reduce the spreading and growth of this invasive species in the Mediterranean and other salt marshes worldwide with little disturbance.
Influence of Environmental Factors on the Variability of Archaeal Communities in a Karst Wetland

Archaea are ubiquitous and play an important role in elemental cycles in Earth’s biosphere; but little is known about their diversity, distribution, abundance, and impact in karst environments. The present study investigated the effect of environmental factors on the variability of archaeal communities in the sediment of the Huixian karst wetland, the largest karst wetland in South China. Sediment cores were obtained from four sampling sites with different water depths and macrophyte inhabitants in both the winter of 2016 and the summer of 2018. The community analysis was based on PacBio sequencing and quantitative PCR of the archaeal 16S rRNA gene. The results showed that Euryarchaeota (57.4%) and Bathyarchaeota (38.7%) were dominant in all the samples. Methanogenic Methanosarcinales (25.1%) and Methanomicrobiales (13.7%), and methanotrophic archaea ANME-2d (9.0%) were the dominant Euryarchaeota; MCG-11 (16.5%), MCG-6 (9.1%), and MCG-5b (5.5%) were the dominant Bathyarchaeota. The community composition remained stable between summer and winter, and the vertical distributions of the archaeal phyla conformed to two patterns among the four sampling sites. In the winter samples, the archaeal 16S rRNA gene abundance was approximately 1.0E+10 copies/g of wet sediment and the Shannon index was 7.3±5, which were significantly higher than in the summer samples and in other karst environments. A correlation analysis showed that the moisture content and pH were the factors that mostly affected the archaeal communities. The prevalence of nitrate in the summer may be a key factor causing a significant decrease in archaeal abundance and diversity. Two features specific to karst environments, calcium-richness and weak alkalescence of the water supplies, may benefit the prevalence of bathyarchaeotal subgroups MCG-11, MCG-5b, and MCG-6. These results suggest that in karst wetlands, most of the archaea belong to clades that have significant roles in carbon turnover; their composition remains stable, but their abundance and diversity vary significantly from season to season.