Miracle-dz/UniFAR-FTUs huggingface dataset:
Automating the analysis of fish abundance using object detection: optimising animal ecology with deep learning

Aquatic ecologists routinely count animals to provide critical information for conservation and management. Increased accessibility to underwater recording equipment such as cameras and unmanned underwater devices have allowed footage to be captured efficiently and safely. It has, however, led to immense volumes of data being collected that require manual processing, and thus significant time, labour and money. The use of deep learning to automate image processing has substantial benefits, but has rarely been adopted within the field of aquatic ecology. To test its efficacy and utility, we compared the accuracy and speed of deep learning techniques against human counterparts for quantifying fish abundance in underwater images and video footage. We collected footage of fish assemblages in seagrass meadows in Queensland, Australia. We produced three models using a MaskR-CNN object detection framework to detect the target species, an ecologically important fish, luderick (Girella tricuspidata). Our models were trained on three randomised 80:20 ratios of training:validation data-sets from a total of 6,080 annotations. The computer accurately determined abundance from videos with high performance using unseen footage from the same estuary as the training data (F1 = 92.4%, mAP50 = 92.5%), and from novel footage collected from a different estuary (F1 = 92.3%, mAP50 = 93.4%). The computer’s performance in determining MaxN was 7.1% better than human marine experts, and 13.4% better than citizen scientists in single image test data-sets, and 1.5% and 7.8% higher in video data-sets, respectively. We show that deep learning is a more accurate tool than humans at determining abundance, and that results are consistent and transferable across survey locations. Deep learning methods provide a faster, cheaper and more accurate alternative to manual data analysis methods currently used to monitor and assess animal abundance. Deep learning techniques have much to offer the field of aquatic ecology.
HEMORRHAGIC PROGRESSION OF CONTUSION IN PATIENTS WITH MILD TRAUMATIC BRAIN INJURY ON THE ROUTINE REPEAT HEAD COMPUTED TOMOGRAPHY

Computed tomography (CT) scan is a standard for the diagnosis of intracranial pathology after traumatic brain injury (TBI). Hemorrhagic progression of contusion (HPC) is frequently seen on repeat CT, but its clinical and radiological significance in case of mild TBI is not well define. The aim of the study: to evaluate the result of routine repeat head CT in patients with mild TBI and brain contusions. Materials and methods: retrospective analysis of management of patients with mild TBI (Glasgow Coma Scale (GCS) score – 13 to 15) and cerebral contusion. All patients were treated at the Kyiv City Clinical Emergency Hospital between 2016 and 2017. Results: within 202 patients with mild TBI, 87 (43.1 %) met the inclusion criteria and were selected for detailed analysis. There were 69 (79.3 %) men and 18 (20.7 %) women. The mean age of the patients was 43.8±12.7 years (17–82 years). The average time between trauma and CT was 3.3 hours. The average volume of contusion on the initial CT was 1.9±0.6 cm3 (0.2–9.6 cm3). The average time of routine CT was 6.8 hours (range 4–24 hours) after the initial scans. HPC was found in 24 (30.7 %) of 87 cases. The average volume of brain contusion on the repeat CT was 2.3±0.5 cm3 (0.2–17.1 cm3). In 3 (3.4 %) patients the size of the hematoma increased. Clinical deterioration occurred in 10 (11.5 %) patients. Six (6.9 %) patients were operated after a CT scan due to HPC with midline shift in 4 cases and increasing of subdural hematoma – 2 cases. Four of these patients had clinical deterioration, and 2 patients were neurological stable. Patients with HPC at admission had lower points of GCS, fractures of the skull (both p<0.001), subdural blood collection (p=0.002), a higher average duration of treatment 8.1±4.2 vs 14.3±5.2 days (p=0.0001), and mortality rate 0 vs. 3 (12.5 %) (p=0.02). Conclusions: Routine repeat CT in patients with mild TBI with brain contusions is aimed to find a patients with s high risk for clinical deterioration. One third of patients with mild TBI and brain contusion experienced HPC. Patients with HPC often have unfavorable clinical course with higher average duration of treatment, delay surgical treatment and mortality rate.
Mps2 links Csm4 and Mps3 to form a telomere-associated LINC complex in budding yeast

The canonical LINC complex is composed of two different transmembrane proteins; this work reveals the heterotrimeric composition of the telomere-associated LINC complex in budding yeast. The linker of the nucleoskeleton and cytoskeleton (LINC) complex is composed of two transmembrane proteins: the KASH domain protein localized to the outer nuclear membrane and the SUN domain protein to the inner nuclear membrane. In budding yeast, the sole SUN domain protein, Mps3, is thought to pair with either Csm4 or Mps2, two KASH-like proteins, to form two separate LINC complexes. Here, we show that Mps2 mediates the interaction between Csm4 and Mps3 to form a heterotrimeric telomere-associated LINC (t-LINC) complex in budding yeast meiosis. Mps2 binds to Csm4 and Mps3, and all three are localized to the telomere. Telomeric localization of Csm4 depends on both Mps2 and Mps3; in contrast, Mps2’s localization depends on Mps3 but not Csm4. Mps2-mediated t-LINC complex regulates telomere movement and meiotic recombination. By ectopically expressing CSM4 in vegetative yeast cells, we reconstitute the heterotrimeric t-LINC complex and demonstrate its ability to tether telomeres. Our findings therefore reveal the heterotrimeric composition of the t-LINC complex in budding yeast and have implications for understanding variant LINC complex formation.
Marine Group II Euryarchaeota Contribute to the Archaeal Lipid Pool in Northwestern Pacific Ocean Surface Waters

Planktonic archaea include predominantly Marine Group I Thaumarchaeota (MG I) and Marine Group II Euryarchaeota (MG II), which play important roles in the oceanic carbon cycle. MG I produce specific lipids called isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs), which are being used in the sea surface temperature proxy named TEX86. Although MG II may be the most abundant planktonic archaeal group in surface water, their lipid composition remains poorly characterized because of the lack of cultured representatives. Circumstantial evidence from previous studies of marine suspended particulate matter suggests that MG II may produce both GDGTs and archaeol-based lipids. In this study, integration of the 16S rRNA gene quantification and sequencing and lipid analysis demonstrated that MG II contributed significantly to the pool of archaeal tetraether lipids in samples collected from MG II-dominated surface waters of the Northwestern Pacific Ocean (NWPO). The archaeal lipid composition in MG II-dominated NWPO waters differed significantly from that of known MG I cultures, containing relatively more 2G-OH-, 2G- and 1G- GDGTs, especially in their acyclic form. Lipid composition in NWPO waters was also markedly different from MG I-dominated surface water samples collected in the East China Sea. GDGTs from MG II-dominated samples seemed to respond to temperature similarly to GDGTs from the MG I-dominated samples, which calls for further study using pure cultures to determine the exact impact of MG II on GDGT-based proxies.
Wnt3 distribution in the zebrafish brain is determined by expression, diffusion and multiple molecular interactions

Wnt3 proteins are lipidated and glycosylated, secreted signaling molecules that play an important role in zebrafish neural patterning and brain development. However, the transport mechanism of lipid-modified Wnts through the hydrophilic extracellular environment for long-range action remains unresolved. Here, we determine how Wnt3 accomplishes long-range distribution in the zebrafish brain. First, we characterize the Wnt3-producing source and Wnt3-receiving target regions. Subsequently, we analyze Wnt3 mobility at different length scales by fluorescence correlation spectroscopy and fluorescence recovery after photo-bleaching. We demonstrate that Wnt3 spreads extracellularly and interacts with heparan sulfate proteoglycans (HSPG). We then determine the binding affinity of Wnt3 to its receptor, Frizzled1 (Fzd1), using fluorescence cross-correlation spectroscopy, and show that the co-receptor, low-density lipoprotein receptor-related protein 5 (Lrp5), is required for Wnt3-Fzd1 interaction. Our results are consistent with the extracellular distribution of Wnt3 by a diffusive mechanism that is modified by tissue morphology, interactions with HSPG and Lrp5-mediated receptor binding, to regulate zebrafish brain development.
The Mammalian Diving Response: Inroads to Its Neural Control

The mammalian diving response (DR) is a remarkable behavior that was first formally studied by Laurence Irving and Per Scholander in the late 1930s. The DR is called such because it is most prominent in marine mammals such as seals, whales, and dolphins, but nevertheless is found in all mammals studied. It consists generally of breathing cessation (apnea), a dramatic slowing of heart rate (bradycardia), and an increase in peripheral vasoconstriction. The DR is thought to conserve vital oxygen stores and thus maintain life by directing perfusion to the two organs most essential for life—the heart and the brain. The DR is important, not only for its dramatic power over autonomic function, but also because it alters normal homeostatic reflexes such as the baroreceptor reflex and respiratory chemoreceptor reflex. The neurons driving the reflex circuits for the DR are contained within the medulla and spinal cord since the response remains after the brainstem transection at the pontomedullary junction. Neuroanatomical and physiological data suggesting brainstem areas important for the apnea, bradycardia, and peripheral vasoconstriction induced by underwater submersion are reviewed. Defining the brainstem circuit for the DR may open broad avenues for understanding the mechanisms of suprabulbar control of autonomic function in general, as well as implicate its role in some clinical states. Knowledge of the proposed diving circuit should facilitate studies on elite human divers performing breath-holding dives as well as investigations on sudden infant death syndrome (SIDS), stroke, migraine headache, and arrhythmias. We have speculated that the DR is the most powerful autonomic reflex known.
Targeting Microglial Population Dynamics in Alzheimer’s Disease: Are We Ready for a Potential Impact on Immune Function?

Alzheimer’s disease (AD) is the most common form of dementia, affecting two-thirds of people with dementia in the world. To date, no disease-modifying treatments are available to stop or delay the progression of AD. This chronic neurodegenerative disease is dominated by a strong innate immune response, whereby microglia plays a central role as the main resident macrophage of the brain. Recent genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) located in microglial genes and associated with a delayed onset of AD, highlighting the important role of these cells on the onset and/or progression of the disease. These findings have increased the interest in targeting microglia-associated neuroinflammation as a potentially disease-modifying therapeutic approach for AD. In this review we provide an overview on the contribution of microglia to the pathophysiology of AD, focusing on the main regulatory pathways controlling microglial population dynamics during the neuroinflammatory response, such as the colony-stimulating factor 1 receptor (CSF1R), its ligands (the colony-stimulating factor 1 and interleukin 34) and the transcription factor PU.1. We also discuss the current therapeutic strategies targeting proliferation to modulate microglia-associated neuroinflammation and their potential impact on peripheral immune cell populations in the short and long-term. Understanding the effects of immunomodulatory approaches on microglia and other immune cell types might be critical for developing specific, effective, and safe therapies for neurodegenerative diseases.
Assessing the Risks of Topically Applied dsRNA-Based Products to Non-target Arthropods

RNA interference (RNAi) is a powerful technology that offers new opportunities for pest control through silencing of genes that are essential for the survival of arthropod pests. The approach relies on sequence-specificity of applied double-stranded (ds) RNA that can be designed to have a very narrow spectrum of both the target gene product (RNA) as well as the target organism, and thus allowing highly targeted pest control. Successful RNAi has been reported from a number of arthropod species belonging to various orders. Pest control may be achieved by applying dsRNA as foliar sprays. One of the main concerns related to the use of dsRNA is adverse environmental effects particularly on valued non-target species. Arthropods form an important part of the biodiversity in agricultural landscapes and contribute important ecosystem services. Consequently, environmental risk assessment (ERA) for potential impacts that plant protection products may have on valued non-target arthropods is legally required prior to their placement on the market. We describe how problem formulation can be used to set the context and to develop plausible pathways on how the application of dsRNA-based products could harm valued non-target arthropod species, such as those contributing to biological pest control. The current knowledge regarding the exposure to and the hazard posed by dsRNA in spray products for non-target arthropods is reviewed and suggestions are provided on how to select the most suitable test species and to conduct laboratory-based toxicity studies that provide robust, reliable and interpretable results to support the ERA.
Engaging Second Language Learners Using the MUSIC Model of Motivation

The overall aim of this article is to explain how the MUSIC Model of Motivation can be applied to L2 instruction in a manner that is consistent with positive psychology, which emphasizes individuals’ strengths and the conditions in which they thrive. The article begins by describing the MUSIC model, which is a research-based framework that organizes strategies that instructors can use to motivate students to engage in learning. The MUSIC model can be used by L2 instructors to create learning experiences that consider learners’ cognition, affect, needs, and desires in order to foster their motivation and engagement in L2 classes. The article also provides teaching strategies related to the MUSIC model and presents an assessment tool (the MUSIC Model of Academic Motivation Inventory) that can be used by L2 instructors to measure students’ MUSIC perceptions of their class. The assessment tool provides feedback to instructors that can be used to improve their instruction by incorporating strategies that allow their students to flourish. Examples of how the MUSIC Inventory can be used to assess L2 instruction are provided. Although researchers have examined the use of the MUSIC model in L2 classes, this research is underdeveloped, and many questions related to its use in L2 classes remain. The article concludes by proposing unanswered questions that could lead to more effective uses of the MUSIC model in L2 classes.
Coordinated evolution between N2 neuraminidase and H1 and H3 hemagglutinin genes increased influenza A virus genetic diversity in swine

The neuraminidase (NA) and hemagglutinin (HA) of influenza A virus (IAV) are essential surface glycoproteins. In this study, the evolution of subtype N2 NA paired with H1 and H3 subtype HA in swine was evaluated to understand if genetic diversity of HA and NA were linked. Using time-scaled Bayesian phylodynamic analyses, the relationships of paired swine N2 with H1 or H3 from 2009 to 2018 were evaluated. These data demonstrated increased relative genetic diversity within the major N2 clades circulating in swine (N2.1998 between 2014-2017 and N2.2002 between 2010-2016). Relative genetic diversity of NA-HA pairs (e.g., N2.1998B/ H1.Delta1B) were correlated, suggesting intergene epistasis. Preferential pairing was observed among specific NA and HA genetic clades and this was associated with gene reassortment between cocirculating influenza A strains. Using the phylogenetic topology of inferred N2 trees, the expansion of genetic diversity in the NA gene was quantified and increases in diversity were observed subsequent to NA-HA reassortment events. The rate of evolution among NA-N2 clades and HA-H1 and HA-H3 clades were similar. The frequent regional movement of pigs and their influenza viruses is a possible explanation driving this pattern of drift, reassortment, and rapid evolution. Bayesian phylodynamic analyses demonstrated strong spatial patterns in N2 genetic diversity, and that frequent interstate movement of N2 clades homogenized diversity. The reassortment and evolution of NA and its influence on HA evolution may affect antigenic drift, impacting vaccine control programs and animal health.
Specific Composition of Lipid Phases Allows Retaining an Optimal Thylakoid Membrane Fluidity in Plant Response to Low-Temperature Treatment

Thylakoid membranes isolated from leaves of two plant species, the chilling tolerant (CT) pea and chilling sensitive (CS) runner bean, were assessed for the composition of lipids, carotenoids as well as for the arrangement of photosynthetic complexes. The response to stress conditions was investigated in dark-chilled and subsequently photo-activated detached leaves of pea and bean. Thylakoids of both species have a similar level of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), but different sulfoquinovosyldiacylglycerol to phosphatidylglycerol (PG) ratio. In pea thylakoid fraction, the MGDG, DGDG and PG, have a higher double bond index (DBI), whereas bean thylakoids contain higher levels of high melting point PG. Furthermore, the lutein to the β-carotene ratio is higher in bean thylakoids. Smaller protein/lipid ratio in pea than in bean thylakoids suggests different lipid-protein interactions in both species. The differences between species are also reflected by the course of temperature-dependent plots of chlorophyll fluorescence pointing various temperatures of the lipid phase transitions of pea and bean thylakoids. Our results showed higher fluidity of the thylakoid membrane network in pea than in bean in optimal temperature conditions. Dark-chilling decreases the photochemical activity and induces significant degradation of MGDG in bean but not in pea leaves. Similarly, substantial changes in the arrangement of photosynthetic complexes with increase in LHCII phosphorylation and disturbances of the thylakoid structure take place in bean thylakoids only. Changes in the physical properties of bean thylakoids are manifested by the conversion of a three-phase temperature-dependent plot to a one-phase plot. Subsequent photo-activation of chilled bean leaves caused a partial restoration of the photochemistry and of membrane physical properties, but not of the photosynthetic complexes arrangement nor the thylakoid network structure. Summarizing, the composition of the thylakoid lipid matrix of CT pea allows retaining the optimal fluidity of its chloroplast membranes under low temperatures. In contrast, the fluidity of CS bean thylakoids is drastically changed, leading to the reorganization of the supramolecular structure of the photosynthetic complexes and finally results in structural remodeling of the CS bean thylakoid network.
Identification and Characterization of a Neutral Locus for Knock-in Purposes in C. parapsilosis

Invasive fungal infections caused by Candida species affect approximately 700,000 people worldwide resulting in 300,000 deaths annually. Besides Candida albicans, other members of the genus have gained relevance in the last two decades, including C. parapsilosis whose incidence is particularly high amongst low birth weight neonates. To investigate the virulence properties of this pathogen several techniques have been developed for generating knock-out mutants, however, no target locus for knock-in approaches have been published so far. Here we report CpNEUT5L (N5L), an intergenic locus in C. parapsilosis, and introduce an integrative GatewayTM and a classical ligation based replacement plasmid to target it with. As a proof of principle, we fluorescently tagged laboratory and prototroph strains and established that this locus is also suitable for reintegration purposes. We concluded that GFP-expressing constructs integrated into this region provide strong, homogenous fluorescent signals while alteration of this locus affects neither the growth of the mutants in liquid or on solid media, even in the presence of different stressors, nor their basic virulence properties. Hence, our findings demonstrate that N5L is a highly effective neutral locus for knock-in approaches in C. parapsilosis.
Elicitation of broadly protective immunity to influenza by multivalent hemagglutinin nanoparticle vaccines

Influenza vaccines that confer broad and durable protection against diverse virus strains would have a major impact on global health. However, next-generation vaccine design efforts have been complicated by challenges including the genetic plasticity of the virus and the immunodominance of certain epitopes in its glycoprotein antigens. Here we show that computationally designed, two-component nanoparticle immunogens induce potently neutralizing and broadly protective antibody responses against a wide variety of influenza viruses. The nanoparticle immunogens display 20 hemagglutinin (HA) trimers in a highly immunogenic array, and their assembly in vitro enables precisely controlled co-display of multiple distinct HAs in defined ratios. Nanoparticle immunogens displaying the four HAs of licensed quadrivalent influenza vaccines (QIV) elicited hemagglutination inhibition and neutralizing antibody responses to vaccine-matched strains that were equivalent or superior to commercial QIV in mice, ferrets, and nonhuman primates. The nanoparticle immunogens—but not QIV—simultaneously induced broadly protective antibody responses to heterologous viruses, including H5N1 and H7N9, by targeting the subdominant yet conserved HA stem. Unlike previously reported influenza vaccine candidates, our nanoparticle immunogens can alter the intrinsic immunodominance hierarchy of HA to induce both potent receptor-blocking and broadly cross-reactive stem-directed antibody responses and are attractive candidates for a next-generation influenza vaccine that could replace current seasonal vaccines. One Sentence Summary Nanoparticle immunogens displaying four seasonal influenza hemagglutinins elicit neutralizing antibodies directed at both the immunodominant head and the conserved stem and confer broad protective immunity.
Functional Improvement of β-Lactoglobulin by Conjugating with Alginate Lyase-Lysate

Bovine β-lactoglobulin−alginic acid oligosaccharide (β-LG−ALGO) conjugate was prepared by the Maillard reaction to improve the function of β-LG. The molar ratio of β-LG to ALGO in the conjugates was 1:7. The isoelectric point of the conjugate was 4.55, which is lower than that of β-LG. Fluorescence studies suggested that the conformation around Trp had changed in the conjugate and that the surface of the conjugate was covered with saccharide chain. Structural analyses with monoclonal antibodies indicated that the conformation around Val15−Ile29 (β-sheet) in the conjugate had changed, while native structure was maintained around Thr125−Lys135 (α-helix). By conjugation with ALGO, β-LG was endowed with high heat stability. The emulsifying activity and the aggregating property of β-LG was improved in the conjugate. Keywords: β-Lactoglobulin; alginic acid; alginate lyase; neoglycoconjugate; functional improvement; acidic polysaccharide; protein conjugation; emulsification; solubility; retinol-binding; lipocalin