Miracle-dz/UniFAR-FTUs huggingface dataset:
An Improved Deep Residual Network Prediction Model for the Early Diagnosis of Alzheimer’s Disease

The early diagnosis of Alzheimer’s disease (AD) can allow patients to take preventive measures before irreversible brain damage occurs. It can be seen from cross-sectional imaging studies of AD that the features of the lesion areas in AD patients, as observed by magnetic resonance imaging (MRI), show significant variation, and these features are distributed throughout the image space. Since the convolutional layer of the general convolutional neural network (CNN) cannot satisfactorily extract long-distance correlation in the feature space, a deep residual network (ResNet) model, based on spatial transformer networks (STN) and the non-local attention mechanism, is proposed in this study for the early diagnosis of AD. In this ResNet model, a new Mish activation function is selected in the ResNet-50 backbone to replace the Relu function, STN is introduced between the input layer and the improved ResNet-50 backbone, and a non-local attention mechanism is introduced between the fourth and the fifth stages of the improved ResNet-50 backbone. This ResNet model can extract more information from the layers by deepening the network structure through deep ResNet. The introduced STN can transform the spatial information in MRI images of Alzheimer’s patients into another space and retain the key information. The introduced non-local attention mechanism can find the relationship between the lesion areas and normal areas in the feature space. This model can solve the problem of local information loss in traditional CNN and can extract the long-distance correlation in feature space. The proposed method was validated using the ADNI (Alzheimer’s disease neuroimaging initiative) experimental dataset, and compared with several models. The experimental results show that the classification accuracy of the algorithm proposed in this study can reach 97.1%, the macro precision can reach 95.5%, the macro recall can reach 95.3%, and the macro F1 value can reach 95.4%. The proposed model is more effective than other algorithms.
Activity-Aware Vital SignMonitoring Based on a Multi-Agent Architecture

Vital sign monitoring outside the clinical environment based on wearable sensors ensures better support in assessing a patient’s health condition, and in case of health deterioration, automatic alerts can be sent to the care providers. In everyday life, the users can perform different physical activities, and considering that vital sign measurements depend on the intensity of the activity, we proposed an architecture based on the multi-agent paradigm to handle this issue dynamically. Different types of agents were proposed that processed different sensor signals and recognized simple activities of daily living. The system was validated using a real-life dataset where subjects wore accelerometer sensors on the chest, wrist, and ankle. The system relied on ontology-based models to address the data heterogeneity and combined different wearable sensor sources in order to achieve better performance. The results showed an accuracy of 95.25% on intersubject activity classification. Moreover, the proposed method, which automatically extracted vital sign threshold ranges for each physical activity recognized by the system, showed promising results for remote health status evaluation.
Associations of MC4R, LEP, and LEPR Polymorphisms with Obesity-Related Parameters in Childhood and Adulthood

MC4R, LEP, and LEPR genes are involved in the hypothalamic leptin-melanocortin regulation pathway, which is important for energy homeostasis. Our study aimed to evaluate the associations between the MC4R rs17782313, LEP rs7799039, and LEPR rs1137101 polymorphisms with obesity-related parameters in childhood and adulthood. The data were obtained from the Kaunas Cardiovascular Risk Cohort study, which started in 1977 with 1082 participants aged 12–13 years. In 2012–2014, the follow-up survey was carried out. Genotype analysis of all respondents (n = 509) aged 48–49 years was performed for the gene polymorphisms using Real-Time Polymerase Chain Reaction. Anthropometric measurements were performed in childhood and adulthood. In childhood, only skinfold thicknesses were associated with gene variants being the lowest in children with MC4R TT genotype and LEP AG genotype. In adulthood, odds of obesity and metabolic syndrome was higher in MC4R CT/CC genotype than TT genotype carriers (OR 1.8; 95% CI 1.2–2.8 and OR 1.6; 95% CI 1.1–2.4, respectively). In men, physical activity attenuated the effect of the MC4R rs17782313 on obesity. The LEP GG genotype was associated with higher BMI, waist circumference, and visceral fat level only in men. No associations of the LEPR rs1137101 polymorphisms with anthropometric measurements and leptin level were found. In conclusion, the associations of the MC4R and LEP gene polymorphisms with obesity-related parameters strengthened with age.
Comparative Analysis of Chloroplast Genomes of Four Medicinal Capparaceae Species: Genome Structures, Phylogenetic Relationships and Adaptive Evolution

This study presents for the first time the complete chloroplast genomes of four medicinal species in the Capparaceae family belonging to two different genera, Cadaba and Maerua (i.e., C. farinosa, C. glandulosa, M. crassifolia and M. oblongifolia), to investigate their evolutionary process and to infer their phylogenetic positions. The four species are considered important medicinal plants, and are used in the treatment of many diseases. In the genus Cadaba, the chloroplast genome ranges from 156,481 bp to 156,560 bp, while that of Maerua ranges from 155,685 bp to 155,436 bp. The chloroplast genome of C. farinosa, M. crassifolia and M. oblongifolia contains 138 genes, while that of C. glandulosa contains 137 genes, comprising 81 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Out of the total genes, 116–117 are unique, while the remaining 19 are replicated in inverted repeat regions. The psbG gene, which encodes for subunit K of NADH dehydrogenase, is absent in C. glandulosa. A total of 249 microsatellites were found in the chloroplast genome of C. farinosa, 251 in C. glandulosa, 227 in M. crassifolia and 233 in M. oblongifolia, the majority of which are mononucleotides A/T found in the intergenic spacer. Comparative analysis revealed variable hotspot regions (atpF, rpoC2, rps19 and ycf1), which can be used as molecular markers for species authentication and as regions for inferring phylogenetic relationships among them, as well as for evolutionary studies. The monophyly of Capparaceae and other families under Brassicales, as well as the phylogenetic positions of the studied species, are highly supported by all the relationships in the phylogenetic tree. The cp genomes reported in this study will provide resources for studying the genetic diversity of Capparaceae, as well as resolving phylogenetic relationships within the family.
Polyhydroxyalkanoate/Antifungal Polyene Formulations with Monomeric Hydroxyalkanoic Acids for Improved Antifungal Efficiency

Novel biodegradable and biocompatible formulations of “old” but “gold” drugs such as nystatin (Nys) and amphotericin B (AmB) were made using a biopolymer as a matrix. Medium chain length polyhydroxyalkanoates (mcl-PHA) were used to formulate both polyenes (Nys and AmB) in the form of films (~50 µm). Thermal properties and stability of the materials were not significantly altered by the incorporation of polyenes in mcl-PHA, but polyene containing materials were more hydrophobic. These formulations were tested in vitro against a panel of pathogenic fungi and for antibiofilm properties. The films containing 0.1 to 2 weight % polyenes showed good activity and sustained polyene release for up to 4 days. A PHA monomer, namely 3-hydroxydecanoic acid (C10-OH), was added to the films to achieve an enhanced synergistic effect with polyenes against fungal growth. Mcl-PHA based polyene formulations showed excellent growth inhibitory activity against both Candida yeasts (C. albicans ATCC 1023, C. albicans SC5314 (ATCC MYA-2876), C. parapsilosis ATCC 22019) and filamentous fungi (Aspergillus fumigatus ATCC 13073; Trichophyton mentagrophytes ATCC 9533, Microsporum gypseum ATCC 24102). All antifungal PHA film preparations prevented the formation of a C. albicans biofilm, while they were not efficient in eradication of mature biofilms, rendering them suitable for the transdermal application or as coatings of implants.
Direct Interaction of Polar Scaffolding Protein Wag31 with Nucleoid-Associated Protein Rv3852 Regulates Its Polar Localization

Rv3852 is a unique nucleoid-associated protein (NAP) found exclusively in Mycobacterium tuberculosis (Mtb) and closely related species. Although annotated as H-NS, we showed previously that it is very different from H-NS in its properties and is distinct from other NAPs, anchoring to cell membrane by virtue of possessing a C-terminal transmembrane helix. Here, we investigated the role of Rv3852 in Mtb in organizing architecture or synthesis machinery of cell wall by protein–protein interaction approach. We demonstrated a direct physical interaction of Rv3852 with Wag31, an important cell shape and cell wall integrity determinant essential in Mtb. Wag31 localizes to the cell poles and possibly acts as a scaffold for cell wall synthesis proteins, resulting in polar cell growth in Mtb. Ectopic expression of Rv3852 in M. smegmatis resulted in its interaction with Wag31 orthologue DivIVAMsm. Binding of the NAP to Wag31 appears to be necessary for fine-tuning Wag31 localization to the cell poles, enabling complex cell wall synthesis in Mtb. In Rv3852 knockout background, Wag31 is mislocalized resulting in disturbed nascent peptidoglycan synthesis, suggesting that the NAP acts as a driver for localization of Wag31 to the cell poles. While this novel association between these two proteins presents one of the mechanisms to structure the elaborate multi-layered cell envelope of Mtb, it also exemplifies a new function for a NAP in mycobacteria.
Comparison of Diazotrophic Composition and Distribution in the South China Sea and the Western Pacific Ocean

Simple Summary Diazotrophs are important contributors of bioavailable nitrogen that is essential to maintaining biological productivity in marine ecosystems. In this study, surface water samples were analyzed to explore the spatial variation of the diazotrophic community in the upper seawater of the South China Sea (SCS) and the Western Pacific Ocean (WPO). The well-conserved gene nifH, which is considered an important marker gene, was used for analyzing the phylogeny, diversity, and abundance of diazotrophs in this study. Our results showed that Proteobacteria was the main diazotroph in the SCS, while Cyanobacteria accounted for the largest proportion in the diazotroph community in the WPO. In addition, high abundances of diazotrophs in the subequatorial WPO indicated the occurrence of diazotrophs blooming. Variation in the composition of diazotrophs was significantly correlated with temperature, dissolved inorganic nitrogen, dissolved inorganic phosphate, and spatial variables between these regions. Our results provide insights into the ecological success and biogeochemical importance of diazotrophic communities in changing environments. Abstract The variation of diazotrophs has been elusive in multiple SCS and WPO regions due to insufficient data. Therefore, the dynamics of diazotrophic composition and distribution were investigated in this study, based on high-throughput sequencing and quantitative PCR of the nifH gene. We found that Proteobacteria dominated the diazotrophic community in the river-impacted SCS and cyanobacteria and Proteobacteria were more abundant in the ocean-dominated SCS and WPO. The qPCR analysis showed that cyanobacterial Trichodesmium was abundant in the Pearl River plume and in the SCS basin influenced by the Kuroshio intrusion, and it also thrived in the subequatorial region of the WPO. Unicellular cyanobacteria UCYN-A were mainly detected in the river-impacted area, UCYN-B was abundant in the WPO, UCYN-C had a relatively high abundance in the ocean-dominated area, and a preponderance of γ-Proteobacteria γ-24774A11 was observed in the ocean-dominated SCS and pelagic WPO. Diazotrophic communities had significant distance–decay relationships, reflecting clear biogeographic patterns in the study area. The variations of diazotrophic community structure were well explained by dissolved inorganic nitrogen, dissolved inorganic phosphate by an eigenvector spatial variable PCNM1. These results provide further information to help determine the ecological mechanism of elusive diazotrophic communities in different ocean ecosystems.
Mechanical Properties and Bioactivity of Polyetheretherketone/Hydroxyapatite/Carbon Fiber Composite Prepared by the Mechanofusion Process

The main obstacles in the melt-processing of hydroxyapatite (HA) and carbon fiber (CF) reinforced polyetheretherketone (PEEK) composite are the high melting temperature of PEEK, poor dispersion of HA nanofillers, and poor processability due to high filler content. In this study, we prepared PEEK/HA/CF ternary composite using two different non-melt blending methods; suspension blending (SUS) in ethanol and mechanofusion process (MF) in dry condition. We compared the mechanical properties and bioactivity of the composite in a spinal cage application in the orthopedic field. Results showed that the PEEK/HA/CF composite made by the MF method exhibited higher flexural and compressive strengths than the composite prepared by the SUS method due to the enhanced dispersibility of HA nanofiller. On the basis of in vitro cell compatibility and cell attachment tests, PEEK/HA/CF composite by mechanofusion process showed an improvement in in vitro bioactivity and osteo-compatibility.
Analysing Parallel Strategies to Alter the Host Specificity of Bacteriophage T7

Simple Summary The problem of antimicrobial resistance is prominent and new alternatives to antibiotics are necessary. Bacteriophages are viruses that target host bacteria and can be used efficiently for their antibacterial properties to solve the problem of antimicrobial resistance. In this study, we explore ways to genetically modify T7 bacteriophage and make its tropism broader, so that it can attack a higher variety of bacteria. We are using different methodologies to achieve this, among of those bacteriophage recombineering using electroporated DNA (BRED), which seems to be the most efficient. Abstract The recognition and binding of host bacteria by bacteriophages is most often enabled by a highly specific receptor–ligand type of interaction, with the receptor-binding proteins (RBPs) of phages being the primary determinants of host specificity. Specifically modifying the RBPs could alter or extend the host range of phages otherwise exhibiting desired phenotypic properties. This study employed two different strategies to reprogram T7 phages ordinarily infecting commensal K12 Escherichia coli strains to infect pathogen-associated K1-capsule-expressing strains. The strategies were based on either plasmid-based homologous recombination or bacteriophage recombineering using electroporated DNA (BRED). Our work pursued the construction of two genetic designs: one replacing the gp17 gene of T7, the other replacing gp11, gp12, and gp17 of T7 with their K1F counterparts. Both strategies displayed successful integration of the K1F sequences into the T7 genome, detected by PCR screening. Multiple methods were utilised to select or enrich for chimeric phages incorporating the K1F gp17 alone, including trxA, host-specificity, and CRISPR-Cas-based selection. Irrespective of the selection method, the above strategy yielded poorly reproducible phage propagation on the new host, indicating that the chimeric phage was less fit than the wild type and could not promote continual autonomous reproduction. Chimeric phages obtained from BRED incorporating gp11-12 and gp17, however, all displayed infection in a 2-stage pattern, indicating the presence of both K1F and T7 phenotypes. This study shows that BRED can be used as a tool to quickly access the potential of new RBP constructs without the need to engineer sustainably replicating phages. Additionally, we show that solely repurposing the primary RBP is, in some cases, insufficient to produce a viable chimeric phage.
Anakinra Activates Superoxide Dismutase 2 to Mitigate Inflammasome Activity

Inflammasomes are powerful cytosolic sensors of environmental stressors and are critical for triggering interleukin-1 (IL-1)-mediated inflammatory responses. However, dysregulation of inflammasome activation may lead to pathological conditions, and the identification of negative regulators for therapeutic purposes is increasingly being recognized. Anakinra, the recombinant form of the IL-1 receptor antagonist, proved effective by preventing the binding of IL-1 to its receptor, IL-1R1, thus restoring autophagy and dampening NLR family pyrin domain containing 3 (NLRP3) activity. As the generation of mitochondrial reactive oxidative species (ROS) is a critical upstream event in the activation of NLRP3, we investigated whether anakinra would regulate mitochondrial ROS production. By profiling the activation of transcription factors induced in murine alveolar macrophages, we found a mitochondrial antioxidative pathway induced by anakinra involving the manganese-dependent superoxide dismutase (MnSOD) or SOD2. Molecularly, anakinra promotes the binding of SOD2 with the deubiquitinase Ubiquitin Specific Peptidase 36 (USP36) and Constitutive photomorphogenesis 9 (COP9) signalosome, thus increasing SOD2 protein longevity. Functionally, anakinra and SOD2 protects mice from pulmonary oxidative inflammation and infection. On a preclinical level, anakinra upregulates SOD2 in murine models of chronic granulomatous disease (CGD) and cystic fibrosis (CF). These data suggest that protection from mitochondrial oxidative stress may represent an additional mechanism underlying the clinical benefit of anakinra and identifies SOD2 as a potential therapeutic target.
Measurement of Ex Vivo Liver, Brain and Pancreas Thermal Properties as Function of Temperature

The ability to predict heat transfer during hyperthermal and ablative techniques for cancer treatment relies on understanding the thermal properties of biological tissue. In this work, the thermal properties of ex vivo liver, pancreas and brain tissues are reported as a function of temperature. The thermal diffusivity, thermal conductivity and volumetric heat capacity of these tissues were measured in the temperature range from 22 to around 97 °C. Concerning the pancreas, a phase change occurred around 45 °C; therefore, its thermal properties were investigated only until this temperature. Results indicate that the thermal properties of the liver and brain have a non-linear relationship with temperature in the investigated range. In these tissues, the thermal properties were almost constant until 60 to 70 °C and then gradually changed until 92 °C. In particular, the thermal conductivity increased by 100% for the brain and 60% for the liver up to 92 °C, while thermal diffusivity increased by 90% and 40%, respectively. However, the heat capacity did not significantly change in this temperature range. The thermal conductivity and thermal diffusivity were dramatically increased from 92 to 97 °C, which seems to be due to water vaporization and state transition in the tissues. Moreover, the measurement uncertainty, determined at each temperature, increased after 92 °C. In the temperature range of 22 to 45 °C, the thermal properties of pancreatic tissue did not change significantly, in accordance with the results for the brain and liver. For the three tissues, the best fit curves are provided with regression analysis based on measured data to predict the tissue thermal behavior. These curves describe the temperature dependency of tissue thermal properties in a temperature range relevant for hyperthermia and ablation treatments and may help in constructing more accurate models of bioheat transfer for optimization and pre-planning of thermal procedures.
Characterization of Burning Behaviors and Particulate Matter Emissions of Crop Straws Based on a Cone Calorimeter

Crop residue burning is one of the major sources of particulate matter (PM) in the air. The burning behaviors and PM emissions of the three typical crop residues (rice straw, wheat straw, corn straw) in China were characterized by a cone calorimeter (CONE) coupled with a laser dust meter. The water-soluble compounds, carbonaceous content, and morphology of PM were measured by ion chromatography, elemental analyzer, transmission electron microscopy (TEM) and energy-dispersive X-ray spectrometer (EDS). The results showed that thermal stability of corn straw was the worst among the three crop straws. The heat release rate (HRR) curves of the three crop straws were the typical curves of thermally thick charring (residue forming) samples. Wheat straw had the highest smoke yield, which was 2.9 times that of rice straw. The PM emission factor of wheat straw was 180.91 µg/g, which was about three times that of rice straw. The contents of K+, Na+, and Cl− in PM were significantly higher than those of the other six water-soluble inorganic ions. The ratio of organic carbon and elemental carbon (OC/EC) ranged from 14.82 to 30.82, which was similar to the results of open burning. There were mainly three kinds of aggregates in the PM of crop straws: network, chain-like, and soot. Individual particles were mixtures of KCl and organic matters. Core-shell structures were found in PM of rice straw and corn straw. The results in this study were provided based on CONE, an ISO-standard apparatus, which could avoid data conflicts caused by the difference of combustion devices. The relationship between the burning behavior and PM emission characteristics of crop straws was established, which is helpful to understand emissions of crop straws and to find a novel way to solve the problems from the burning of crop residues.
A System Using Artificial Intelligence to Detect and Scare Bird Flocks in the Protection of Ripening Fruit

Flocks of birds may cause major damage to fruit crops in the ripening phase. This problem is addressed by various methods for bird scaring; in many cases, however, the birds become accustomed to the distraction, and the applied scaring procedure loses its purpose. To help eliminate the difficulty, we present a system to detect flocks and to trigger an actuator that will scare the objects only when a flock passes through the monitored space. The actual detection is performed with artificial intelligence utilizing a convolutional neural network. Before teaching the network, we employed videocameras and a differential algorithm to detect all items moving in the vineyard. Such objects revealed in the images were labeled and then used in training, testing, and validating the network. The assessment of the detection algorithm required evaluating the parameters precision, recall, and F1 score. In terms of function, the algorithm is implemented in a module consisting of a microcomputer and a connected videocamera. When a flock is detected, the microcontroller will generate a signal to be wirelessly transmitted to the module, whose task is to trigger the scaring actuator.