Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecosystem Services and Cash Crop Tradeoffs of Summer Cover Crops in Northern Region Organic Vegetable Rotations

Intensive production practices characterizing vegetable farming contribute to high productivity, but often at the expense of supporting and regulating ecosystem services. Diversification with cover crops may support increased resilience through soil organic matter (SOM) contributions and physical soil protection. Vegetable farming often includes spring and fall production, limiting establishment and productive potential of over-wintered cover crops that are more widely used in the USA. In northern climate vegetable systems, warm-season cover crops planted during short summer fallows could be a tool to build resilience via ecosystem service enhancement. This project evaluated summer cover crops in the northern USA (MN and WI) for biomass accumulation, weed suppression, and contribution to fall cash crop yield. Our study included four site years, during which we investigated the effects of four cover crop species treatments, grown for 30 (short duration, SD) or 50 days (long duration, LD) alongside bare fertilized and unfertilized control treatments: buckwheat (Fagopyrum esculentum) and sunn hemp (Crotalaria juncea) monocultures, and biculture of chickling vetch (Lathyrus sativus) or cowpea (Vigna unguiculata) with sorghum-sudangrass (sudex) (Sorghum bicolor x S. bicolor var. Sudanese). To quantify cover crop quantity, quality, and weed suppression capacity, we measured cover crop and weed biomass, and biomass C:N. To quantify effects on cash crops, we measured fall broccoli yield and biomass. Mean total biomass (cover crop + weeds) by site year ranged from 1,890 kg ha−1 in MN Y1 to 5,793 kg ha−1 in WI Y2 and varied among species in Y1 for both the SD and LD treatments. Most cover crops did not outcompete weeds, but treatments with less weeds produced more overall biomass. Data from Y1 show that cover crops were unable to replace fertilizer for fall broccoli yield, and led to reduced fall crop yield. Broccoli in Y2 did not reach maturity due to fall freeze. Summer cover crops, because of their biomass accumulation potential, may be used by farmers in northern climates to fit into cropping system niches that have historically been left as bare soil, but care with timing is necessary to optimize weed suppression and mitigate tradeoffs for cash crop production.
Advances in Oral Drug Delivery

The oral route is the most common route for drug administration. It is the most preferred route, due to its advantages, such as non-invasiveness, patient compliance and convenience of drug administration. Various factors govern oral drug absorption including drug solubility, mucosal permeability, and stability in the gastrointestinal tract environment. Attempts to overcome these factors have focused on understanding the physicochemical, biochemical, metabolic and biological barriers which limit the overall drug bioavailability. Different pharmaceutical technologies and drug delivery systems including nanocarriers, micelles, cyclodextrins and lipid-based carriers have been explored to enhance oral drug absorption. To this end, this review will discuss the physiological, and pharmaceutical barriers influencing drug bioavailability for the oral route of administration, as well as the conventional and novel drug delivery strategies. The challenges and development aspects of pediatric formulations will also be addressed.
Exogenous Aspergillus aculeatus Enhances Drought and Heat Tolerance of Perennial Ryegrass

Perennial ryegrass (Lolium perenne) is a cool-season grass whose growth and development are limited by drought and high temperature. Aspergillus aculeatus has been reported to promote plant growth and counteract the adverse effects of abiotic stresses. The objective of this study was to assess A. aculeatus-induced response mechanisms to drought and heat resistance in perennial ryegrass. We evaluated the physiological and biochemical markers of drought and heat stress based on the hormone homeostasis, photosynthesis, antioxidant enzymes activity, lipid peroxidation, and genes expression level. We found out that under drought and heat stress, A. aculeatus-inoculated leaves exhibited higher abscisic acid (ABA) and lower salicylic acid (SA) contents than non-inoculated regimes. In addition, under drought and heat stress, the fungus enhanced the photosynthetic performance, decreased the antioxidase activities, and mitigated membrane lipid peroxidation compared to non-inoculated regime. Furthermore, under drought stress, A. aculeatus induced a dramatic upregulation of sHSP17.8 and DREB1A and a downregulation of POD47, Cu/ZnSOD, and FeSOD genes. In addition, under heat stress, A. aculeatus-inoculated plants exhibited a higher expression level of HSP26.7a, sHSP17.8, and DREB1A while a lower expression level of POD47 and FeSOD than non-inoculated ones. Our results provide an evidence of the protective role of A. aculeatus in perennial ryegrass response to drought and heat stresses.
DriverSubNet: A Novel Algorithm for Identifying Cancer Driver Genes by Subnetwork Enrichment Analysis

Identification of driver genes from mass non-functional passenger genes in cancers is still a critical challenge. Here, an effective and no parameter algorithm, named DriverSubNet, is presented for detecting driver genes by effectively mining the mutation and gene expression information based on subnetwork enrichment analysis. Compared with the existing classic methods, DriverSubNet can rank driver genes and filter out passenger genes more efficiently in terms of precision, recall, and F1 score, as indicated by the analysis of four cancer datasets. The method recovered about 50% more known cancer driver genes in the top 100 detected genes than those found in other algorithms. Intriguingly, DriverSubNet was able to find these unknown cancer driver genes which could act as potential therapeutic targets and useful prognostic biomarkers for cancer patients. Therefore, DriverSubNet may act as a useful tool for the identification of driver genes by subnetwork enrichment analysis.
Characterization of an Antiviral Component in Human Seminal Plasma

Numerous types of viruses have been found in human semen, which raises concerns about the sexual transmission of these viruses. The overall effect of semen on viral infection and transmission have yet to be fully investigated. In the present study, we aimed at the effect of seminal plasma (SP) on viral infection by focusing on the mumps viral (MuV) infection of HeLa cells. MuV efficiently infected HeLa cells in vitro. MuV infection was strongly inhibited by the pre-treatment of viruses with SP. SP inhibited MuV infection through the impairment of the virus’s attachment to cells. The antiviral activity of SP was resistant to the treatment of SP with boiling water, Proteinase K, RNase A, and DNase I, suggesting that the antiviral factor would not be proteins and nucleic acids. PNGase or PLA2 treatments did not abrogate the antiviral effect of SP against MuV. Further, we showed that the prostatic fluid (PF) showed similar inhibition as SP, whereas the epididymal fluid and seminal vesicle extract did not inhibit MuV infection. Both SP and PF also inhibited MuV infection of other cell types, including another human cervical carcinoma cell line C33a, mouse primary epididymal epithelial cells, and Sertoli cell line 15P1. Moreover, this inhibitory effect was not specific to MuV, as the herpes simplex virus 1, dengue virus 2, and adenovirus 5 infections were also inhibited by SP and PF. Our findings suggest that SP contains a prostate-derived pan-antiviral factor that may limit the sexual transmission of various viruses.
Incidental Brain Magnetic Resonance Imaging Findings and the Cognitive and Motor Performance in the Elderly: The Shanghai Changfeng Study

Background The frequently discovered incidental findings (IFs) from imaging observations are increasing. The IFs show the potential clues of structural abnormalities underlying cognitive decline in elders. Detecting brain IFs and their relationship with cognitive and behavioral functions helps provide the information for clinical strategies. Methods Five hundred and seventy-nine participants were recruited in the Shanghai Changfeng Study. All participants performed the demographic, biochemical, and cognitive functions and gait speed assessment and underwent the high-resolution multimodal magnetic resonance imaging scans. We calculated the detection rate of brain IFs. The association between cardiovascular risk factors and IFs and the associations between IFs and cognitive and motor functions were assessed using regression models. The relationships among gray matter volume, cognitive function, and gait speed were assessed with/without adjusting the IFs to evaluate the effects of potential IFs confounders. Results IFs were found in a total of 578 subjects with a detection rate of 99.8%. Age and blood pressure were the most significant cardiovascular risk factors correlated with IFs. IFs were found to be negatively associated with Montreal Cognitive Assessment, Mini-Mental State Examination, and gait speed. The gray matter volume was found to be positively correlated with the cognitive function without adjusting the white matter hyperintensity but not if adjusted. Conclusion IFs are commonly found in the elderly population and related to brain functions. The adequate intervention of IFs related cardiovascular risk factors that may slow down the progression of brain function decline. We also suggest that IFs should be considered as confounding factors that may affect cognitive issues on the structural neuroimaging researches in aging or diseases.
nMNSD—A Spiking Neuron-Based Classifier That Combines Weight-Adjustment and Delay-Shift

The recent “multi-neuronal spike sequence detector” (MNSD) architecture integrates the weight- and delay-adjustment methods by combining heterosynaptic plasticity with the neurocomputational feature spike latency, representing a new opportunity to understand the mechanisms underlying biological learning. Unfortunately, the range of problems to which this topology can be applied is limited because of the low cardinality of the parallel spike trains that it can process, and the lack of a visualization mechanism to understand its internal operation. We present here the nMNSD structure, which is a generalization of the MNSD to any number of inputs. The mathematical framework of the structure is introduced, together with the “trapezoid method,” that is a reduced method to analyze the recognition mechanism operated by the nMNSD in response to a specific input parallel spike train. We apply the nMNSD to a classification problem previously faced with the classical MNSD from the same authors, showing the new possibilities the nMNSD opens, with associated improvement in classification performances. Finally, we benchmark the nMNSD on the classification of static inputs (MNIST database) obtaining state-of-the-art accuracies together with advantageous aspects in terms of time- and energy-efficiency if compared to similar classification methods.
Characterization of Polyhydroxyalkanoates Produced at Pilot Scale From Different Organic Wastes

Polyhydroxyalkanoates (PHAs) production at pilot scale has been recently investigated and carried out exploiting different process configurations and organic wastes. More in detail, three pilot platforms, in Treviso (North-East of Italy), Carbonera (North-East of Italy) and Lisbon, produced PHAs by open mixed microbial cultures (MMCs) and different organic waste streams: organic fraction of municipal solid waste and sewage sludge (OFMSW-WAS), cellulosic primary sludge (CPS), and fruit waste (FW), respectively. In this context, two stabilization methods have been applied, and compared, for preserving the amount of PHA inside the cells: thermal drying and wet acidification of the biomass at the end of PHA accumulation process. Afterward, polymer has been extracted following an optimized method based on aqueous-phase inorganic reagents. Several PHA samples were then characterized to determine PHA purity, chemical composition, molecular weight, and thermal properties. The polymer contained two types of monomers, namely 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) at a relative percentage of 92.6–79.8 and 7.4–20.2 w/w, respectively, for Treviso and Lisbon plants. On the other hand, an opposite range was found for 3HB and 3HV monomers of PHA from Carbonera, which is 44.0–13.0 and 56.0–87.0 w/w, respectively. PHA extracted from wet-acidified biomass had generally higher viscosity average molecular weights (Mv) (on average 424.8 ± 20.6 and 224.9 ± 21.9 KDa, respectively, for Treviso and Lisbon) while PHA recovered from thermally stabilized dried biomass had a three-fold lower Mv.
Gastrodin Inhibits Virus Infection by Promoting the Production of Type I Interferon

Type I interferon (IFN-I) plays a critical role in the antiviral immune response. However, viruses have developed different strategies to suppress the production of IFN-I for its own escape and amplification. Therefore, promoting the production of IFN-I is an effective strategy against virus infection. Gastrodin (GTD), a phenolic glucoside extracted from Gastrodia elata Blume, has been reported to play a protective role in some central nervous system -related diseases and is beneficial for the recovery of diseases by inhibiting inflammation. However, the effect of GTD on virus infection is largely unknown. Here we found GTD treatment increased the survival rate of mice infected with vesicular stomatitis virus (VSV) or herpes simplex virus-1 (HSV-1). The production of IFN-I was increased in GTD-treated mice or macrophages compared to the control group, during virus infection. Furthermore, the activation of interferon regulatory factor 3 (IRF3) was promoted by GTD in macrophages upon VSV and HSV-1 infection. Our results demonstrated that GTD could inhibit the VSV and HSV-1 infection by promoting the production of IFN-I in macrophages and might provide an effective strategy against virus infection.
Acute Physiological and Psychological Stress Response in Youth at Clinical High-Risk for Psychosis

Deficits in stress-response systems are a characteristic of schizophrenia and psychosis spectrum illnesses, and recent evidence suggests that this impairment may be evident in those at clinical high-risk (CHR) for the development of a psychotic disorder. However, there is limited research specifically investigating biological and subjective stress reactivity in CHR individuals. In the present study, 38 CHR individuals and group of 38 control individuals participated in the Trier Social Stress Test (TSST), an experimentally induced psychosocial stressor. Changes in salivary cortisol and alpha amylase, as well as self-reported units of distress (SUDS), were evaluated. Interestingly, the TSST did not induce a change in cortisol levels in either group, though the CHR group did show higher overall cortisol levels throughout the TSST (pre-anticipation period through recovery period). However, indicative of an effective task manipulation, the TSST did illicit an increase in alpha amylase in both groups. CHR participants exhibited higher levels of subjective stress prior to the stressor compared to the control group and CHR SUDs did not significantly increase in response to the stressor. In contrast, the control group showed an increase in SUDS in response to the stressor. Notably, SUDS for the control group post task mirrored the levels CHR youth endorsed prior to the stressor. Taken together, these findings suggest that there may be a functional relationship between persistently elevated cortisol and chronic high levels of subjective distress in CHR individuals.
Tumor Immune Microenvironment Characterization in Hepatocellular Carcinoma Identifies Four Prognostic and Immunotherapeutically Relevant Subclasses

Purpose The tumor microenvironment (TME) plays a critical role in the pathogenesis of hepatocellular carcinoma (HCC). However, underlying compositions and functions that drive the establishment and maintenance of the TME classifications are less-well understood. Methods A total of 766 HCC patients from three public cohorts were clustered into four immune-related subclasses based on 13 TME signatures (11 immune-related cells and 2 immune-related pathways) calculated by MCP-counter. After analyzing the landscapes of functional annotation, methylation, somatic mutation, and clinical characteristics, we built a TME-based Support Vector Machine of 365 patients (discovery phase) and 401 patients (validation phase). We applied this SVM model on another two independent cohorts of patients who received sorafenib/pembrolizumab treatment. Results About 33% of patients displayed an immune desert pattern. The other subclasses were different in abundance of tumor infiltrating cells. The Immunogenic subclass (17%) associated with the best prognosis presented a massive T cell infiltration and an activation of immune checkpoint pathway. The 13 TME signatures showed a good potential to predict the TME classification (average AUC = 88%). Molecular characteristics of immunohistochemistry from Zhejiang cohort supported our SVM classification. The optimum response to pembrolizumab (78%) and sorafenib (81%) was observed in patients belonging to the Immunogenic subclass. Conclusions The HCC patients from distinct immune subclass showed significant differences in clinical prognosis and response to personalized treatment. Based on tumor transcriptome data, our workflow can help to predict the clinical outcomes and to find appropriate treatment strategies for HCC patients.
Patterns of Sediment Fungal Community Dependent on Farming Practices in Aquaculture Ponds

Despite fungi playing an important role in nutrient decomposition in aquatic ecosystems and being considered as vital actors in the ecological processes, they received limited attention regarding the community in aquaculture pond sediments which are extremely important and typically disturbed habitats. Using an ITS1 region of fungal rDNA, this study aimed to investigate sediment fungal communities in fish, crab, and crayfish ponds for decades of farming practices at representative aquaculture regions in the middle Yangtze River basin, China. We then aimed to explore the community patterns associated with species-based farming practices in the ponds at 18 farms. The results showed that the pond sediments harbored more than 9,000 operational taxonomic units. The sediments had significantly higher alpha diversity in crab ponds compared to that in fish and crayfish ponds. The fungal phyla largely belonged to Ascomycota and Chytridiomycota, and the dominance of Rozellomycota over Basidiomycota and Aphelidiomycota was observed. The majority of sediment fungal members were ascribed to unclassified fungi, with higher proportions in fish ponds than crab and crayfish ponds. Further, the fungal communities were markedly distinct among the three types of ponds, suggesting divergent patterns of fungal community assemblages caused by farming practices in aquaculture ponds. The community diversity and structure were closely correlated to sediment properties, especially sediment carbon content and pH. Thus, the distribution and pattern of fungal communities in the sediments appear to primarily depend on species-based farming practices responsible for the resulting sediment carbon content and pH in aquaculture ponds. This study provides a detailed snapshot and extension of understanding fungal community structure and variability in pond ecosystems, highlighting the impacts of farming practices on the assembly and succession of sediment fungal communities in aquaculture ponds.
12-Tungstosilicic Acid Supported on Different Carriers: Pronounced Catalytic Activity in the Synthesis of Bis(indolyl)methanes Under Solvent-Free Conditions

12-Tungstosilicic acid supported on different metal oxides was used as catalyst in the synthesis of bis(indolyl)methanes via electrophilic substitution reactions of indole with structurally diverse aldehydes and cyclohexanone. The effects of solvent, catalyst loading, and the nature of substituents on the aromatic ring of aldehydes were investigated. The workup of the reaction consists of simple filtration, followed by concentration of the crude product, and purification. A mechanism for the catalytic activity is proposed, and corresponding products were obtained in good to excellent yields in relatively short reaction times. The catalysts were reusable without significant loss of activity.
Similar Yield Benefits of Hybrid, Conventional, and Organic Tomato and Sweet Pepper Varieties Under Well-Watered and Drought-Stressed Conditions

Global agrobiodiversity is threatened by the replacement of traditional, locally adapted crop varieties with high-yielding and hybrid varieties during the past 60 years, resulting in associated losses of crop, variety, and allele diversity. Locally adapted, traditional varieties are known to perform equal or even better under environmental stress conditions and to be more resilient in unstable cultivation environments. Therefore, European organic vegetable breeding organizations conserve local, traditional varieties and breed new varieties in low-input organic environments, aiming to increase the range of varieties for sustainable cultivation under sub-optimal growing conditions. However, performance of organic vegetable varieties, in comparison to conventional high-yielding and hybrid varieties, under different environmental conditions has not been intensively researched. To contribute to this scientific field, we compared the agronomic and quality performance between hybrid, conventional, and organic tomato and sweet pepper varieties, two economically important species on the EU market under a) well-watered and b) drought stress conditions, using five different varieties (i.e., 30 varieties) as replicates in each of the six groups. Performance of both species was negatively affected by drought, regardless of the breeding background. Equally, for tomato and sweet pepper, hybrids produced higher amounts of individual fruits, however total yield in kg was comparable for hybrid, conventional and organic plants. Considering the agro-ecological importance of enlarging and securing variety diversity in light of changing environmental conditions, we show that the assumed benefits of the hybrids can also be delivered by the organic and conventional varieties. These varieties should be considered as an important source of genetic resources, supporting farmers to adapt to their local climate and environmental conditions in the future.