Miracle-dz/UniFAR-FTUs huggingface dataset:
An Underwater Organism Image Dataset and A Lightweight Module Designed for Object Detection Networks

Long-term monitoring and recognition of underwater organism objects are of great significance in marine ecology, fisheries science and many other disciplines. Traditional techniques in this field, including manual fishing-based ones and sonar-based ones, are usually flawed. Specifically, the method based on manual fishing is time-consuming and unsuitable for scientific researches, while the sonar-based one, has the defects of low acoustic image accuracy and large echo errors. In recent years, the rapid development of deep learning and its excellent performance in computer vision tasks make vision-based solutions feasible. However, the researches in this area are still relatively insufficient in mainly two aspects. First, to our knowledge, there is still a lack of large-scale datasets of underwater organism images with accurate annotations. Second, in consideration of the limitation on hardware resources of underwater devices, an underwater organism detection algorithm that is both accurate and lightweight enough to be able to infer in real time is still lacking. As an attempt to fill in the aforementioned research gaps to some extent, we established the Multiple Kinds of Underwater Organisms (MKUO) dataset with accurate bounding box annotations of taxonomic information, which consists of 10,043 annotated images, covering eighty-four underwater organism categories. Based on our benchmark dataset, we evaluated a series of existing object detection algorithms to obtain their accuracy and complexity indicators as the baseline for future reference. In addition, we also propose a novel lightweight module, namely Sparse Ghost Module, designed especially for object detection networks. By substituting the standard convolution with our proposed one, the network complexity can be significantly reduced and the inference speed can be greatly improved without obvious detection accuracy loss. To make our results reproducible, the dataset and the source code are available online at https://cslinzhang.github. io/MKUO-and-Sparse-Ghost-Module/.
Stężenia wybranych metali ciężkich w osadach dennych cieku wodnego

The research was carried out on the section of the watercourse located in the village Mostowo. Watercourse flows through the pipe at a certain distance. The study was carried out on the uncanalized part with length of 1022 m. At this section the three measuring points were established. Bottom sediments were analyzed for the contents of selected heavy metals, such as: Cd, Co, Cr, Cu, Ni, Pb, Zn. Using the maximum concentrations of heavy metals in the analyzed sediment samples the evaluation of watercourse sediment contamination was done. The aim of the study was the assessment of sediments contamination and indication on possibilities of their utilization. The obtained results indicate that the highest concentrations of heavy metals in the sediments were in samples taken from a point located near the business buildings, allotments and near the seed headquarters (P-1) in a layers 5-10 and 20-30 cm. The results indicate that the studied sediments differently accumulated the heavy metals depending on the location of sampling points. That accumulation can be expressed by different series of heavy metals concentration in the sediment. For the point P 1 it takes the following form: Zn> Pb> Cu> Cr> Ni> Co> Cd, for the point P-2: Zn> Cu> Cr> Ni> Pb> Co> Cd and for the point P-3 the series is as follows: Zn> Cu> Cr> Pb> Ni> Co> Cd. Bottom sediments can be classified into first and second water quality class. They can be freely utilized in aquatic and terrestrial environments.
Demise of Ediacaran dolomitic seas marks widespread biomineralization on the Siberian Platform

The trigger for biomineralization of metazoans in the terminal Ediacaran, ca. 550 Ma, has been suggested to be the rise of oxygenation or an increase in seawater Ca concentration, but geochemical and fossil data have not been fully integrated to demonstrate cause and effect. Here we combine the record of macrofossils with early marine carbonate cement distribution within a relative depth framework for terminal Ediacaran to Cambrian successions on the eastern Siberian Platform, Russia, to interrogate the evolution of seawater chemistry and biotic response. Prior to ca. 545 Ma, the presence of early marine ferroan dolomite cement suggests dominantly ferruginous anoxic "aragonite-dolomite seas", with a very shallow oxic chemocline that supported mainly soft-bodied macrobiota. After ca. 545 Ma, marine cements changed to aragonite and/or high-Mg calcite, and this coincides with the appearance of widespread aragonite and high-Mg calcite skeletal metazoans, suggesting a profound change in seawater chemistry to "aragonite seas" with a deeper chemocline. By early Cambrian Stage 3, the first marine low-Mg calcite cements appear, coincident with the first low-Mg calcite metazoan skeletons, suggesting a further shift to "calcite seas". We suggest that this evolution of seawater chemistry was caused by enhanced continental denudation that increased the input of Ca into oceans so progressively lowering Mg/Ca, which, combined with more widespread oxic conditions, facilitated the rise of skeletal animals and in turn influenced the evolution of skeletal mineralogy.
Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects using Simulations

The process of domestication involves a complex interplay between concurrent demographic and selective changes. While we can readily observe the phenotypic effects of domestication, the genetic consequences of domestication often remain elusive. Artificial selection can alter the selection coefficients of both new and pre-existing genetic variation within domesticated populations. To investigate this, we conducted simulations using a combination of population genomic parameters designed to reflect the domestication process observed in large livestock mammals. Our study uses forward-in-time simulations to examine the 1D and 2D site frequency spectra (SFS) of mutations in two populations that have diverged since the domestication split. In total, we examined eighteen different scenarios, varying the strength of selection acting on beneficial mutations and the proportion of mutations with altered selection coefficients post-domestication. First, we discuss how linked selection and fluctuating selection coefficients affect the accuracy of inferred demographic histories. Second, we find that certain aspects of the full distribution of fitness effects (DFE), such as the shape and strength of the deleterious DFE, can be accurately estimated in both populations using only the 1D-SFS. However, the accurate characterization of the beneficial DFE remains a challenge, even when using the 2D-SFS. Third, using a novel joint DFE model, we are able to quantify the fraction of mutations that have experienced a change in their selection coefficient (pc) during domestication. Interestingly, classic hard selective sweeps can mimic a substantial increase in pc, even when the simulated pc was initially zero. In summary, our work highlights the strengths and limitations of detecting changes in the DFE, and emphasizes the risks of over- interpreting demographic histories across a range of realistic domestication scenarios.
Methane and ethane production rates by methyl-coenzyme M reductase in cell extracts from different methanogens

Methyl-Coenzyme M reductase (Mcr) plays an important role in the regulation of the global carbon cycle. The enzyme catalyzes the reversible conversion of methyl-coenzyme M and coenzyme B to methane and the corresponding heterodisulfide CoM-S-S-CoB, which constitutes the first step of the anaerobic oxidation of methane. Mcr homologs of varies methanogenic archaea also catalyze the anaerobic oxidation of extended alkanes. Fully active, purified enzyme is exclusively achievable via strictly anaerobic purification from Methanothermobacter marburgensis. This microbe expresses two isoenzymes and most studies were performed with isoenzyme I that exhibits a limited substrate-promiscuity (c.a. 0.5%) towards the homologous substrate ethyl-coenzyme M. Here, cell-free lysates from the different species such as Methanosarcina mazei, Methanococcus maripaludis, Methanothermococcus okinawansis, and Mt. marburgensis were screened for Mcr activity and substrate promiscuity. An assay relying on titanium (III) citrate and cobalamin to regenerate coenzyme B and coenzyme M was used to test the ability of different cell extracts for the catalytic activity towards the C2-substrate ethyl-coenzyme M. Cell extracts from M. mazei showed a ratio of ethane-to methane-production of ca. 8% at 37 °C, and about 14% at 49 °C. The level of substrate-promiscuity towards ethyl-coenzyme M for M. marburgensis cell extracts under our assay conditions were much higher than previously reported for purified isoenzyme I, indicating that isoenzyme II is much more promiscuous for ethane formation than isoenzyme I. Our experiments demonstrate that Mcr activity can be quickly and conveniently studied via cell-free lysates, and that substrate promiscuity towards ethane formation is generally larger than anticipated.
From juveniles to giants: Drivers of holobiont assembly in massive Porites

The fate of coral reefs in response to climate change depends on their ability to adapt to new environments. The coral animal is buffered from environmental stress by its algal endosymbionts and microbial partners (together, the “holobiont”). However, the flexibility of holobiont community assembly in time and space is not well understood, making it difficult to estimate its contribution to coral adaptation. To clarify these processes at a centuries-long time scale, we compared the holobiont of massive Porites adults (>2m) to their juvenile (<30cm) counterparts across environments. We genotyped coral hosts from Orpheus Island, Australia and characterized their associated Symbiodiniaceae and bacterial communities. We recovered ten distinct genetic clusters of the coral host, reflecting the known difficulty in identifying species of massive Porites compounded by cryptic genetic structure. Within the largest of these clusters, we additionally found significant genetic separation between adult and juvenile corals. Host genetic structure was the primary driver of both Symbiodiniaceae (84% of variance explained) and microbial (60% of variance explained) community composition, indicating strong holobiont specificity in cryptic lineages. The relative role of environment and age was over two-fold higher for the microbial community compared to the Symbiodiniaceae community. Our results indicate local environmental factors and time influence the microbial community at a meaningful scale, but genetics trumps all for the vertically-transmitted Symbiodiniaceae community.
Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of Ψ at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a Ψ-to-C transition. Compared to previous methods, BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS successfully detected all known Ψ sites in human rRNA and spliceosomal snRNAs and generated the first quantitative Ψ map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites and N1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant Ψ114 site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of Ψ in future studies.
A conserved Pol II elongator SPT6L mediates Pol V transcription elongation to regulate RNA-directed DNA methylation in Arabidopsis

In plants, the plant-specific RNA polymerase V (Pol V) transcripts non-coding RNAs and provides a docking platform for the association of accessory proteins in the RNA-directed DNA methylation (RdDM) pathway. Various components have been uncovered that are involved in the process of DNA methylation, but it is still not clear how the transcription of Pol V is regulated. Here, we found that the conserved Pol II elongator, SPT6L, bound to thousands of intergenic regions in an RNA polymerase II (Pol II) independent manner. The intergenic enrichment of SPT6L, interestingly, co-occupied with the largest subunit of Pol V (NRPE1) and mutation of SPT6L led to the reduction of DNA methylation but not Pol V enrichment. Furthermore, the association of SPT6L at Pol V loci was dependent on the Pol V associated factor, SPT5L, rather than the presence of Pol V, and the interaction between SPT6L and NRPE1 was compromised in spt5l. Finally, Pol V RIP-seq revealed that SPT6L is required to maintain the amount and length of Pol V transcripts. Our findings thus uncovered the critical role of a Pol II conserved elongator in Pol V mediated DNA methylation and transcription, and shed light on the mutual regulation between Pol V and II in plants.
Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria

Diverse bacteria and archaea use atmospheric carbon monoxide (CO) as an energy source during long-term survival. This process enhances the biodiversity of soil and marine ecosystems globally and removes 250 million tonnes of a toxic, climate-relevant pollutant from the atmosphere each year. Bacteria use [MoCu]-carbon monoxide dehydrogenases (Mo-CODH) to convert CO to carbon dioxide, then transfer the liberated high-energy electrons to the aerobic respiratory chain. However, given no high-affinity Mo-CODH has been purified, it is unknown how these enzymes oxidise CO at low concentrations and interact with the respiratory chain. Here we resolve these knowledge gaps by analysing Mo-CODH (CoxSML) and its hypothetical partner CoxG from Mycobacterium smegmatis. Kinetic and electrochemical analyses show purified Mo-CODH is a highly active high-affinity enzyme (Km = 139 nM, kcat = 54.2 s-1). Based on its 1.85 Å resolution cryoEM structure, Mo-CODH forms a CoxSML homodimer similar to characterised low-affinity homologs, but has distinct active site coordination and narrower gas channels that may modulate affinity. We provide structural, biochemical, and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain via the membrane-bound menaquinone-binding protein CoxG. Consistently, CoxG is required for CO-driven respiration, extracts menaquinone from mycobacterial membranes, and binds quinones in a hydrophobic pocket. Finally, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of a biogeochemically and ecologically important process, while demonstrating that the newly discovered process of long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.
RFX6 at locus 6q22 confers metastasis and drug resistance in prostate cancer

Genetic and nonmutational epigenetic alterations are cancer hallmark characteristics. However, the role of inherited cancer predisposition alleles in co-opting lineage factor epigenetic reprogramming and contributing to tumor progression remains elusive. Here the FinnGen cohort phenome-wide analysis, along with recent multiple genome-wide association studies, has consistently identified the rs339331-RFX6/6q22 locus associated with prostate cancer (PCa) risk across diverse populations. We uncover that rs339331 resides at a reprogrammed androgen receptor (AR) binding site in PCa tumors, with the T risk allele enhancing AR chromatin occupancy under androgen signaling. We establish that RFX6 is an AR-regulated gene, intricately linked with rs339331, exhibiting synergistic prognostic value for PCa recurrence and metastasis. Through comprehensive in vitro and in vivo studies, we establish the oncogenic functions of RFX6 in promoting PCa cell proliferation and metastasis. Mechanistically, RFX6 upregulates transcription factor HOXA10 that profoundly correlates with adverse PCa outcomes and is pivotal in RFX6-mediated PCa progression, facilitating the epithelial-mesenchymal transition (EMT) process and modulating the TGFβ/SMAD signaling axis. Clinically, HOXA10 elevation is associated with increased EMT scores, tumor advancement and PCa recurrence. Remarkably, reducing RFX6 expression restores responsiveness of enzalutamide-resistant PCa cells and tumors to treatment. Our study highlights an interplay of disrupted genetic and epigenetic mechanisms converging on prostate lineage AR signaling, resulting in abnormal expression of RFX6 conferring PCa pathogenesis and enzalutamide resistance.
Enhancement of mediodorsal thalamus rescues aberrant belief dynamics in a mouse model with schizophrenia-associated mutation

Optimizing behavioral strategy requires belief updating based on new evidence, a process that engages higher cognition. In schizophrenia, aberrant belief dynamics may lead to psychosis, but the mechanisms underlying this process are unknown, in part, due to lack of appropriate animal models and behavior readouts. Here, we address this challenge by taking two synergistic approaches. First, we generate a mouse model bearing patient-derived point mutation in Grin2a (Grin2aY700X+/−), a gene that confers high-risk for schizophrenia and recently identified by large-scale exome sequencing. Second, we develop a computationally trackable foraging task, in which mice form and update belief-driven strategies in a dynamic environment. We found that Grin2aY700X+/− mice perform less optimally than their wild-type (WT) littermates, showing unstable behavioral states and a slower belief update rate. Using functional ultrasound imaging, we identified the mediodorsal (MD) thalamus as hypofunctional in Grin2aY700X+/− mice, and in vivo task recordings showed that MD neurons encoded dynamic values and behavioral states in WT mice. Optogenetic inhibition of MD neurons in WT mice phenocopied Grin2aY700X+/− mice, and enhancing MD activity rescued task deficits in Grin2aY700X+/− mice. Together, our study identifies the MD thalamus as a key node for schizophrenia-relevant cognitive dysfunction, and a potential target for future therapeutics.
Nutraceutical Potential of Seaweed Polysaccharides: Structure, Bioactivity, Safety, and Toxicity.

In recent years, marine organisms including seaweeds have been highlighted as potential sources of useful metabolites and bioactive compounds, with vast biological and physiological activities. Seaweeds have long been used as a food source, for medicinal purposes, and as dietary supplements in various Asian countries, and their potential benefits have recently attracted the attention of many Western and European countries. Their commercial value depends on their applications in the food, nutraceutical, and pharmaceutical industries. Seaweeds are considered a potential source of nutraceuticals or functional foods, and analysis of taste-oriented motives has revealed that seaweeds are preferentially selected over other types of marine foods by seafood consumers and people with high levels of health, education, and living status. It is a general perception that health conscious people prefer environmentally friendly food sources, and present an opportunity to focus on seaweed-based foods, which have significant nutritional benefits to humans. Among the various bioactive constituents, seaweed polysaccharides have been proven to possess various beneficial properties including anticoagulant, anti-inflammatory, antioxidant, anticarcinogenic, and antiviral activities. The diversity and composition of seaweed polysaccharides play vital roles in these biological activities. Seaweeds are a rich source of sulfated polysaccharides, which are responsible for much of the bioactivity, as they can interact with various textures and cellular proteins. A number of toxicological assays and clinical trials suggest that the ingestion of seaweeds as functional foods should be considered worldwide to improve immune responses. In this review, different polysaccharides from seaweeds and their compositions and potential nutraceutical applications are discussed.
Discriminative Topics Modelling for Action Feature Selection and Recognition

This paper presents a framework for recognising realistic human actions captured from unconstrained environments. The novelties of this work lie in three aspects. First, we propose a new action representation based on computing a rich set of descriptors from key point trajectories. Second, in order to cope with drastic changes in motion characteristics with and without camera movements, we develop an adaptive feature fusion method to combine different local motion descriptors for improving model robustness against feature noise and background clutters. Finally, we propose a novel Multi-Class Delta Latent Dirichlet Allocation model for feature selection. The most informative features in a high dimensional feature space are selected collaboratively, rather than independently as by existing feature selection methods. Extensive experiments on challenging public datasets demonstrate the effectiveness of the proposed framework.
Person Re-Identification by Support Vector Ranking

Solving the person re-identification problem involves matching observations of individuals across disjoint camera views. The problem becomes particularly hard in a busy public scene as the number of possible matches is very high. This is further compounded by significant appearance changes due to varying lighting conditions, viewing angles and body poses across camera views. To address this problem, existing approaches focus on extracting or learning discriminative features followed by template matching using a distance measure. The novelty of this work is that we reformulate the person reidentification problem as a ranking problem and learn a subspace where the potential true match is given highest ranking rather than any direct distance measure. By doing so, we convert the person re-identification problem from an absolute scoring problem to a relative ranking problem. We further develop an novel Ensemble RankSVM to overcome the scalability limitation problem suffered by existing SVM-based ranking methods. This new model reduces significantly memory usage therefore is much more scalable, whilst maintaining high-level performance. We present extensive experiments to demonstrate the performance gain of the proposed ranking approach over existing template matching and classification models.
EFFECT OF SOWING DATE ON THE YIELD AND SUGAR CONTENT OF SUGAR BEET AND FODDER BEET AT FOUR SITES

Fodder beet and sugar beet were sown on 4 to 6 dates between late August and mid December 1980 at 4 sites in Canterbury. On 2 irrigated sites, sugar yields were 15 to 17 t/ha for late August and early September sowings, thereafter sugar yields declined at a rate of over 100 kg/ha for each day sowing was delayed. On non-irrigated sites, sugar yields for equivalent early September sowings were 450Jo lower than for irrigated sites but declined more slowly with later sowing to become equal to irrigated sites from late November. Sowing date had little effect on root sugar content. There was little difference in sugar yield between sugar beet and fodder beet because, despite the fodder beet yielding 35% more root fresh weight, its sugar content was 27% lower.