Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate Multilevel Classification for Wildlife Images

The most common approaches for classification rely on the inference of a specific class. However, every category could be naturally organized within a taxonomic tree, from the most general concept to the specific element, and that is how human knowledge works. This representation avoids the necessity of learning roughly the same features for a range of very similar categories, and it is easier to understand and work with and provides a classification for each abstraction level. In this paper, we carry out an exhaustive study of different methods to perform multilevel classification applied to the task of classifying wild animals and plant species. Different convolutional backbones, data setups, and ensembling techniques are explored to find the model which provides the best performance. As our experimentation remarks, in order to achieve the best performance on the datasets that are arranged in a tree-like structure, the classifier must feature an EfficientNetB5 backbone with an input size of 300 × 300 px, followed by a multilevel classifier. In addition, a Multiscale Crop data augmentation process must be carried out. Finally, the accuracy of this setup is a 62% top-1 accuracy and 88% top-5 accuracy. The architecture could benefit for an accuracy boost if it is involved in an ensemble of cascade classifiers, but the computational demand is unbearable for any real application.
Field–Frequency-Dependent Non-linear Rheological Behavior of Magnetorheological Grease Under Large Amplitude Oscillatory Shear

This article investigates the influence of frequency on the field-dependent non-linear rheology of magnetorheological (MR) grease under large amplitude oscillatory shear (LAOS). First, the LAOS tests with different driving frequencies were conducted on MR grease at four magnetic fields, and the storage and loss moduli under the frequency of 0.1, 0.5, 1, and 5 Hz were compared to obtain an overall understanding of the frequency-dependent viscoelastic behavior of MR grease. Based on this, the three-dimensional (3D) Lissajous curves and decomposed stress curves under two typical frequencies were depicted to provide the non-linear elastic and viscous behavior. Finally, the elastic and viscous measures containing higher harmonics from Fourier transform (FT)-Chebyshev analysis were used to quantitatively interpret the influence of the frequency on the non-linear rheology of MR grease, namely, strain stiffening (softening) and shear thickening (thinning), under LAOS with different magnetic fields. It was found that, under the application of the magnetic field, the onset of the non-linear behavior of MR grease was frequency-dependent. However, when the shear strain amplitude increased in the post-yield region, the non-linear rheology of MRG-70 was not affected by the oscillatory frequency.
Gold Nanoparticles in Cancer Theranostics

Conventional cancer treatments, such as surgical resection, radiotherapy, and chemotherapy, have achieved significant progress in cancer therapy. Nevertheless, some limitations (such as toxic side effects) are still existing for conventional therapies, which motivate efforts toward developing novel theranostic avenues. Owning many merits such as easy surface modification, unique optical properties, and high biocompatibility, gold nanoparticles (AuNPs and GNPs) have been engineered to serve as targeted delivery vehicles, molecular probes, sensors, and so on. Their small size and surface characteristics enable them to extravasate and access the tumor microenvironment (TME), which is a promising solution to realize highly effective treatments. Moreover, stimuli-responsive properties (respond to hypoxia and acidic pH) of nanoparticles to TME enable GNPs’ unrivaled control for effective transport of therapeutic cargos. In this review article, we primarily introduce the basic properties of GNPs, further discuss the recent progress in gold nanoparticles for cancer theranostics, with an additional concern about TME stimuli-responsive studies.
Effects of Microbial Inoculation and Storage Length on Fermentation Profile and Nutrient Composition of Whole-Plant Sorghum Silage of Different Varieties

This study aimed to assess the effects of a heterofermentative microbial inoculant and storage length on fermentation profile, aerobic stability, and nutrient composition in whole-plant sorghum silage (WPSS) from different varieties. Experiment 1, a completely randomized design with a 2 × 3 factorial treatment arrangement, evaluated microbial inoculation [CON (50 mL distilled water) or LBLD (Lactobacillus plantarum DSM 21762, L. buchneri DSM 12856, and L. diolivorans DSM 32074; 300,000 CFU/g of fresh forage)] and storage length (14, 28, or 56 d) in forage WPSS. The LBLD silage had lower pH compared to CON, and greater concentrations of succinic acid, ethanol, 1,2-propanediol (1,2-PD), 1-propanol, 2,3-butanediol and total acids. After 56 d, lactic acid concentration was greater for CON, while acetic acid and aerobic stability were greater in LBLD silage. Experiment 2, a completely randomized design with a 2 × 3 factorial treatment arrangement, evaluated effects of microbial inoculation (same as experiment 1) and storage length (14, 28, or 56 d) in WPSS of three varieties [forage sorghum (Mojo Seed, OPAL, Hereford, TX), sorghum-sudangrass (Dyna-gro Seed, Fullgraze II, Loveland, CO, United States), or sweet sorghum (MAFES Foundation Seed Stocks, Dale, MS State, MS)]. The LBLD forage sorghum had greater acetic acid and 1,2-PD concentrations at 56 d and 28 d, respectively, but lower concentrations of propionic acid at 56 d and butyric acid at 14 and 28 d. Additionally, WSC concentration was greater for CON than LBLD at 28 d. Furthermore, CON sweet sorghum had greater lactic acid, propionic acid, and butyric acid concentrations. However, greater acetic acid and 1,2-PD were observed for LBLD sweet sorghum. The CON sweet sorghum had greater concentration of WSC and yeast counts. The CON sorghum sudangrass had greater lactic and butyric acid concentrations than LBLD at 14 d, but lower acetic acid and 1,2-PD concentrations at 56 d. Yeast counts were greater for CON than LBLD sorghum sudangrass silage. Overall, results indicate inoculation of WPSS with Lactobacillus plantarum DSM 21762, L. buchneri DSM 12856, and L. diolivorans DSM 32074 improves heterofermentative co-fermentation allowing the accumulation of acetic acid concentration and increasing antifungal capacities and aerobic stability of WPSS.
Networks in the Field of Tourette Syndrome

Gilles de la Tourette syndrome (TS) is a neuropsychiatric neurodevelopmental disorder with the cardinal clinical features of motor and phonic tics. Clinical phenomenology can be complex since, besides tics, there are other features including premonitory urges preceding tics, pali-, echo-, and coprophenomena, hypersensitivity to external stimuli, and symptom dependency on stress, attention, and other less well-defined factors. Also, the rate of comorbidities, particularly attention deficit hyperactivity disorder and obsessive-compulsive disorder, is high. Mirroring the complexities of the clinical course and phenomenology, pathophysiological findings are very diverse, and etiology is disputed. It has become clear, though, that abnormalities in the basal ganglia and their connections with cortical areas are key for the understanding of the pathophysiology and as regards etiology, genetic factors are crucial. Against this background, both adequate clinical management of TS and TS-related research require multidisciplinary preferably international cooperation in larger groups or networks to address the multiple facets of this disorder and yield valid and useful data. In particular, large numbers of patients are needed for brain imaging and genetic studies. To meet these requirements, a number of networks and groups in the field of TS have developed over the years creating an efficient, lively, and supportive international research community. In this review, we will provide an overview of these groups and networks.
Conservation Implications of Sabellaria spinulosa Reef Patches in a Dynamic Sandy-Bottom Environment

Biogenic reefs form biodiversity hotspots and are key components of marine ecosystems, making them priority habitats for nature conservation. However, the conservation status of biogenic reefs generally depends on their size and stability. Dynamic, patchy reefs may therefore be excluded from protection. Here, we studied epibenthos and epifauna density, richness, and community composition of patchy, dynamic Sabellaria spinulosa (ross worm) reefs in the North Sea. This study was conducted by comparing boxcore (endobenthos) and video transect (epifauna) data from two research campaigns in 2017 and 2019 to the Brown Bank area on the Dutch Continental Shelf, where S. spinulosa reefs were first discovered in 2017. The Brown Bank area is characterized by dynamic, migratory bedforms at multiple scales which potentially affect biogenic reef stability. We showed that S. spinulosa habitats had a patchy distribution and alternated with habitats comprised of plain sand. Average S. spinulosa habitat patch size was 5.57 ± 0.99 m and 3.94 ± 0.22 m in 2017 and 2019, respectively (mean ± SE), which especially in 2019 closely resembled the small-scale megaripple bedforms. Contrary to the endobenthos communities that were unaffected by S. spinulosa, epifauna density and species richness were at least two times higher in S. spinulosa habitats compared to sandy habitats, resulting in different community compositions between the two habitat types. We showed that S. spinulosa persisted in the area for almost 2 years. Although the stability of individual patches remained unclear, we demonstrated that even patchy biogenic reefs may promote density and local biodiversity of mobile, epibenthic species, very likely as a result of increased habitat heterogeneity provided by reef habitat patches. This indicates that patchy biogenic reefs that occur in dynamic environments may also have high ecological value and their conservation status should be (re)considered to ensure their protection.
Systemic Expression, Purification, and Initial Structural Characterization of Bacteriophage T4 Proteins Without Known Structure Homologs

Bacteriophage T4 of Escherichia coli is one of the most studied phages. Research into it has led to numerous contributions to phage biology and biochemistry. Coding about 300 gene products, this double-stranded DNA virus is the best-understood model in phage study and modern genomics and proteomics. Ranging from viral RNA polymerase, commonly found in phages, to thymidylate synthase, whose mRNA requires eukaryotic-like self-splicing, its gene products provide a pool of fine examples for phage research. However, there are still up to 130 gene products that remain poorly characterized despite being one of the most-studied model phages. With the recent advancement of cryo-electron microscopy, we have a glimpse of the virion and the structural proteins that present in the final assembly. Unfortunately, proteins participating in other stages of phage development are absent. Here, we report our systemic analysis on 22 of these structurally uncharacterized proteins, of which none has a known homologous structure due to the low sequence homology to published structures and does not belong to the category of viral structural protein. Using NMR spectroscopy and cryo-EM, we provided a set of preliminary structural information for some of these proteins including NMR backbone assignment for Cef. Our findings pave the way for structural determination for the phage proteins, whose sequences are mainly conserved among phages. While this work provides the foundation for structural determinations of proteins like Gp57B, Cef, Y04L, and Mrh, other in vitro studies would also benefit from the high yield expression of these proteins.
Medical Students' Voluntary Service During the COVID-19 Pandemic in Poland

From the very first moment coronavirus struck, medical students volunteered to support healthcare professionals' fight against the COVID-19 pandemic. To learn more about future healthcare professionals' volunteering during such an outbreak, we conducted a survey among 417 students of Poznan University of Medical Sciences. Our findings suggest that although numerous studies demonstrate that traditional, value-based volunteering is decreasing, and especially higher education students are more oriented toward their own career, in the times of the current health crisis, young peoples' involvement in volunteering has been mainly driven by altruism and the ethical imperative to serve their community, their fellow healthcare professionals and their patients. Thus, while the prime role of the volunteering was to relieve the healthcare system, it also reinforced such important medical values as altruism, public service and professional solidarity. Moreover, it proved that whilst risk is inherent to medicine, the students' volunteering is truly a moral enterprise.
Only Females Oviposit: Chemical Discrimination of Adult Stink Bug Sex by the Egg Parasitoid Trissolcus japonicus

Egg parasitoids foraging for suitable hosts scattered in the environment rely mainly on chemical cues. Elucidating the chemical ecology of natural enemies is important in the development of effective and successful strategies for conservation biological control. In this context, the host cuticular hydrocarbons, which are exploited by several species of egg parasitoids as contact kairomones, could be used to retain them by providing information about the presence and the sex of adults of the target species: sex is important because only females of the host species lay the eggs that can be subsequently utilized for parasitoid reproduction. However, the chemical basis of host sex discrimination in egg parasitoids is not well understood. We carried out behavioral and chemical bioassays to investigate the role played by contact chemical cues left by adults of the brown marmorated stink bug, Halyomorpha halys Stål, in host egg searching behavior and adult host sex discrimination by the egg parasitoid Trissolcus japonicus (Ashmead). A first set of bioassays showed that parasitoids spent more time exploring patches contaminated with chemicals associated with adult H. halys females compared with adult males. Similar responses were displayed by T. japonicus when hexane extracts of H. halys were tested suggesting that non-polar chemical compounds are involved in host sex discrimination. GC-MS analysis of hexane extracts revealed quantitative differences in the cuticular compounds of the two sexes, with 1-hexadecene (more abundant in males) being the most important component in determining these differences. Hexane extracts of H. halys females blended with synthetic 1-hexadecene significantly reduced the wasps’ arrestment responses compared to crude extracts.
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.
LCZ696 Attenuated Doxorubicin-Induced Chronic Cardiomyopathy Through the TLR2-MyD88 Complex Formation

Background and Purpose The profibrotic and proinflammatory effects induced by doxorubicin (DOX) are key processes in the development of serious heart damage. Lack of effective drugs and the unclear mechanisms of its side effects limit the clinical treatment of DOX-induced cardiac injury. This study aimed to explore the protective role of LCZ696 and the potential mechanism of Toll-like receptor 2 (TLR2) in doxorubicin-induced cardiac failure. Experimental Approach DOX (5 mg/kg/week, three times) was used to establish a chronic cardiomyopathy mouse model. Heart function tests, pathology examinations and molecular biology analyses were used to explore the effects of LCZ696 and TLR2 deficiency in vivo and in vitro. Computational docking was applied to predict the key residues for protein-ligand interaction. Key Results The EF% declined, and the LVIDd, pro-fibrosis marker levels and NF-κB related inflammatory response increased in the chronic cardiomyopathy group induced by DOX. LCZ696 treatment and TLR2 deficiency reversed these heart damage in vivo. In H9C2 cells, pre-treatment with LCZ696 and TLR2 knockdown suppressed the DOX-induced high expression of profibrotic and proinflammatory markers. Moreover, DOX notably increased the TLR2-MyD88 interaction in vivo and in vitro, which was inhibited by LCZ696. Finally, we demonstrated the direct interaction between DOX and TLR2 via hydrogen bonds on Pro-681 and Glu-727 and Pro-681 and Ser-704 may be the key residues by which LCZ696 affects the interaction between DOX and TLR2. Conclusion and Implications LCZ696 prevents DOX-induced cardiac dilation failure, fibrosis and inflammation by reducing the formation of TLR2-MyD88 complexes. LZC696 may be a potential effective drug to treat DOX-induced heart failure.
LncRNA ST7-AS1 is a Potential Novel Biomarker and Correlated With Immune Infiltrates for Breast Cancer

Background: Long noncoding RNA (lncRNA) ST7-AS1 can be observed in various cancers, but its role in breast cancer (BRC) remains unclear. Our aim is to, on the basis of The Cancer Genome Atlas (TCGA) database, prove the correlation between lncRNA ST7-AS1 and BRC. Methods: The lncRNA ST7-AS1 expression and its roles in the prognosis of BRC were explored using data from the TCGA database. The expression level of lncRNA ST7-AS1 in BRC samples was detected using RT-PCR. The 1-, 3-, or 5-year survival rate was predicted using a nomogram established through Cox proportional hazard regression. At last, the biological function was explored through gene ontology (GO) analysis and gene set enrichment analysis (GSEA). The hallmark pathways significantly involved in hub genes were described through functional enrichment analysis. The correlation between lncRNA ST7-AS1 expression and immune infiltration was analyzed through single-sample GSEA (ssGSEA). Results: LncRNA ST7-AS1 expression was downregulated in BRC. Decreased lncRNA ST7-AS1 expression in BRC was correlated with advanced clinical pathologic characteristics (high grade, histological type, age, menopause status, and HER2 status), survival time, and poor prognosis. The nomogram was established for using lncRNA ST7-AS1 to predict 1-, 3-, or 5-year survival in patients with BRC. In addition, GO and pathway analyses suggested the involvement of lncRNA ST7-AS1 in cell cycle, DNA repair, and immune cell infiltration in the BRC immune microenvironment. We found the correlation of lncRNA ST7-AS1 with T helper cells and DC cells. Conclusion: Low expression of lncRNA ST7-AS1 indicates poor prognosis and has an impact on cell cycle, DNA repair, and proportion of infiltrating immune cells in the BRC microenvironment. Therefore, lncRNA ST7-AS1 can be used as a protective prognostic marker and a potential treatment target for BRC.
Neuroprotective Effects of Oxymatrine on PI3K/Akt/mTOR Pathway After Hypoxic-Ischemic Brain Damage in Neonatal Rats

Oxymatrine (OMT), a quinolizidine alkaloid extracted from traditional Chinese herb Sophora flavescens Ait, has drawn attention because of its beneficial bioactivities against hypoxic–ischemic brain damage (HIBD). However, the underlying molecular mechanism remains unclear. In this study, we determined the in vivo and in vitro effects of OMT on seven-day old Sprague–Dawley rats with HIBD and in a rat model of primary hippocampal neuron oxygen glucose deprivation reoxygenation (OGD/R). This study was aimed to evaluate whether OMT exerted neuroprotective effects mediated by the (phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin) PI3K/Akt/mTOR pathway after HIBD. Experimental results showed that the alkaloid significantly improved the early neurofunctional development, brain water content, abnormal pathological changes, and necrosis of neurons after HIBD. Moreover, OMT enhanced the cell viability and stabilized the mitochondrial permeability transition pore in the primary hippocampal neurons after OGD/R. OMT significantly decreased the autophagosome generation, elevated the expression of PI3K, Akt, and mTOR, and simultaneously reversed the mRNA expression of microtubule-associated protein 1-light chain 3 (LC3), Beclin-1, and sequestosomel (P62) induced by hypoxia and ischemia. However, these protective effects against HIBD could be suppressed when rapamycin, a specific inhibitor of mTOR, was included. Hence, the OMT exerted neuroprotective effects against HIBD by attenuating excessive autophagy by mediating the PI3K/Akt/mTOR pathway.