Miracle-dz/UniFAR-FTUs huggingface dataset:
Community coalescence altered the potential of horizontal gene transfers within the native soil microbiome

Microbial community coalescence, which refers to the mixing of microbial communities, frequently shapes the assemblage of soil microbiomes in natural ecosystems. It can exert selective pressure on the coalescent taxa, leading to ecological changes in microbial community structure or microbial evolutionary changes via horizontal gene transfer (HGT). However, the influence of community coalescence on the potential of HGTs within native communities, particularly in soil ecosystems, remains poorly understood. Here, we experimentally quantified the potential evolutionary consequences of soil coalescence. We achieved that by subjecting microcosms containing natural soil to invasion by several microbial communities and profiling mobile genetic elements (MGEs) and adaptive genes of microbial communities up to 60 days after coalescence. Our findings revealed both specific and common responses of MGEs to coalescences over time. Specific effects differed across invasive communities and were particularly pronounced in the early stages. Common effects were associated with an increased abundance of insertion sequences (ISs) across different treatments, suggesting that ISs played a crucial role in promoting diversification at the community level. In summary, we showed that changing MGE profiles are an intrinsic response of the soil microbial community to coalescence-imposed pressure. Our study provides new insights into the modulation of adaptability in soil microbial communities by utilizing community coalescences to address global challenges.
Single-cell Herpes Simplex Virus type-1 infection of neurons using drop-based microfluidics reveals heterogeneous replication kinetics

Single-cell analyses of viral infections often reveal heterogeneity that is not detected by traditional population-level studies. This study applies drop-based microfluidics to investigate the dynamics of HSV-1 infection of neurons at the single-cell level. We used micron-scale Matrigel beads, termed microgels, to culture individual murine Superior Cervical ganglia (SCG) neurons or epithelial cells. Microgel-cultured cells are subsequently enclosed in individual media-in-oil droplets with a dual fluorescent-reporter HSV-1, enabling real-time observation of viral gene expression and replication. Infection within drops revealed that the kinetics of initial viral gene expression and replication were dependent on the inoculating dose. Notably, increasing inoculating doses led to earlier onset of viral gene expression and more frequent productive viral replication. These observations provide crucial insights into the complexity of HSV-1 infection in neurons and emphasize the importance of studying single-cell outcomes of viral infection. The innovative techniques presented here for cell culture and infection in drops provide a foundation for future virology and neurobiology investigations.
FLATWORM TRANSCRIPTOMES REVEAL WIDESPREAD PARASITISM BY HISTOPHAGOUS CILIATES

Unicellular ciliates like Tetrahymena are best known as free-living bacteriovores, but many species are facultative or obligate parasites. These ‘histophages’ feed on the tissues of hosts ranging from planarian flatworms to commercially important fish and the larvae of imperiled freshwater mussels. Here, we developed a novel bioinformatics pipeline incorporating the nonstandard ciliate genetic code and used it to search for Ciliophora sequences in 34 publicly available Platyhelminthes EST libraries. From 2,615,036 screened ESTs, we identified nearly 6,000 high-confidence ciliate transcripts, supporting parasitism of seven additional flatworm species. We also cultured and identified Tetrahymena from nine terrestrial and freshwater planarians, including invasive earthworm predators from the genus Bipalium and the widely studied regeneration models Dugesia japonica and Schmidtea mediterranea. A cophylogenetic reconstruction provides strong evidence for coevolution of histophagous Ciliophora with their Platyhelminthes hosts. We further report the antiprotozoal aminoglycoside paromomycin expels Tetrahymena from S. mediterranea, providing new opportunities to investigate the effects of this relationship on planarian biology. Together, our findings raise the possibility that invasive flatworms constitute a novel dispersal mechanism for Tetrahymena parasites and position the Platyhelminthes as an ideal model phylum for studying the ecology and evolution of histophagous ciliates.
Transposable element abundance subtly contributes to lower fitness in maize

Transposable elements (TEs) have long been shown to have deleterious effects on the survival and reproduction of their host organism. As TEs are mobile DNA that jump to new positions, this deleterious cost can occur directly, by inserting into genes and regulatory sequences. Classical population genetic theory suggests copy-number dependent selection against TEs is necessary to prevent TEs from expanding so much they take over a genome. Such models have been difficult to interpret when applied to large genomes like maize, where there are hundreds of thousands of TE insertions that collectively make up 85% of the genome. Here, we use nearly 5000 inbred lines from maize mapping populations and a pan-genomic imputation approach to measure TE content. Segregating TE content gives rise to 100 Mb differences between individuals, and populations often show transgressive segregation in TE content. We use replicated phenotypes measured in hybrids across numerous years and environments to empirically measure the fitness costs of TEs. For an annual plant like maize, grain yield is not only a key agronomic phenotype, but also a direct measure of reproductive output. We find weak negative effects of TE accumulation on grain yield, nearing the limit of the efficacy of natural selection in maize. This results in a loss of one kernel (≈0.1% of average per-plant yield) for every additional 14 Mb of TE content. This deleterious load is enriched in TEs within 1 kilobase of genes and young TE insertions. Together, we provide rare empirical measurements of the fitness costs of TEs, and suggest that the TEs we see today in the genome have been filtered by selection against their deleterious consequences on maize fitness.
Circular RNA profiling identifies circ5078 as a BMPR2-derived regulator of endothelial translation

Germline loss-of-function BMPR2 mutations are the leading genetic cause of pulmonary arterial hypertension (PAH) and are strongly linked to aberrant endothelial proliferation and impaired translational stress responses. While these effects are generally attributed to a loss of the type-II bone morphogenetic protein receptor (BMPR-II), we used circular RNA profiling to identify circ5078, a BMPR2-derived circular RNA that regulates endothelial translation and cellular phenotype. circ5078 and linear BMPR2 mRNA exert opposing effects on endothelial proliferation and stress granule formation, while influencing the translational efficiency of multiple genes by regulating ribosome assembly and translational initiation. In PAH patient-derived endothelial cells lacking linear BMPR2 mRNA, circ5078 depletion rescued impaired translational stress responses by rebalancing circular to linear transcript levels, independent of BMPR-II protein. By identifying circ5078 as a functional BMPR2 gene product, this work reveals interdependent roles for both linear and circular BMPR2 transcripts as regulators endothelial translation and proliferation.
Thermo- and photoreceptors of eyes as regulators of circadian rhythm and glymphatic system

The dynamics of hydrogen bonds in bulk and hydrated water affected the activation energies of temperature dependence of ion currents of voltage-dependent channels that regulate communication and trophic bonds in the neuropil of the cortical parenchyma. The physics of minimizing of isobaric heat capacity of water made it possible to explain stabilization and functional optimization of thermodynamics of eyeball fluids at 34.5 °C and human brain during sleep at 36.5 °C. At these temperatures, thermoreceptors of cornea and cells of ganglionic layer of the retina, through connections with suprachiasmatic nucleus and pineal gland, switch brain metabolism from daytime to nighttime modes. The phylogenesis of circadian rhythm was reflected in dependence of duration of nighttime sleep of mammals on diameter of eyeball, mass of pineal gland, and density of neurons in parenchyma of cortex. The activity of all nerves of eyeball led to division of nocturnal sleep into slow and fast phases. These phases correspond to two modes of glymphatic system - electrochemical and dynamic. The first is responsible for relaxation processes of synaptic plasticity and chemical neutralization of toxins with participation of water and melatonin. Rapid eye movement and an increase in cerebral blood flow in second mode increase water exchange in parenchyma and flush out toxins into venous system.
Neural correlates of visual object recognition in rats

Invariant object recognition—the ability to recognize objects across size, rotation, or context—is fundamental for making sense of a dynamic visual world. Although initially believed to be unique to primates due to its complexity, emerging evidence suggests rodents, too, can recognize objects across a range of identity-preserving transformations. Here, we describe a comprehensive pipeline for investigating visual behavior in rats, from high-throughput training to cellular resolution imaging in awake, head-fixed animals. Using this suite of tools, we demonstrate that rats excel in visual object recognition and explore potential neural pathways which may support this capacity. We leverage our optical approach to systematically profile multiple visual areas with responses to a range of stimulus types recorded in the same neurons. Primary and higher-order areas of rat visual cortex exhibit a hierarchical organization consistent with a role in visual object recognition. However, marked deviations from the functional organization of primate visual cortex suggest species-specific differences in the neural circuits underlying visual object recognition. This work reinforces the notion that rats possess sophisticated visual abilities and offers the technical foundation for their use as a powerful model to link neuronal responses to perception and behavior.
Revealing principles of autonomous thermal soaring in windy conditions using vulture-inspired deep reinforcement-learning

Thermal soaring, a technique used by birds and gliders to utilize updrafts of hot air, is an appealing model-problem for studying motion control and how it is learned by animals and engineered autonomous systems. Thermal soaring has rich dynamics and nontrivial constraints, yet it uses few control parameters and is becoming experimentally accessible. Following recent developments in applying reinforcement learning methods for training deep neural-network (deep-RL) models to soar autonomously both in simulation and real gliders, here we develop a simulation-based deep-RL system to study the learning process of thermal soaring. We find that this process has learning bottlenecks, we define a new efficiency metric and use it to characterize learning robustness, we compare the learned policy to data from soaring vultures, and find that the neurons of the trained network divide into function clusters that evolve during learning. These results pose thermal soaring as a rich yet tractable model-problem for the learning of motion control.
Auranofin Induces Lethality Driven by Reactive Oxygen Species in High-Grade Serous Ovarian Cancer Cells

High-grade serous ovarian cancer (HGSOC) accounts for 70% of ovarian cancer cases in the clinical setting; the survival rate for this disease remains remarkably low due to the lack of long-term consolidation therapies following the standard platinum-based chemotherapy, which is not long lasting as the disease recurs as platinum resistant. The purpose of this study was to explore a novel treatment against HGSOC using the gold complex auranofin (AF). AF primarily functions as a pro-oxidant agent through the inhibition of thioredoxin reductase (TrxR), an antioxidant enzyme that is overexpressed in ovarian cancer. We investigated the effect of AF on TrxR activity and various mechanisms of cytotoxicity using HGSOC cells that are clinically sensitive or resistant to platinum. In addition, we studied the interaction between AF and another pro-oxidant agent, L-buthionine sulfoximine (L-BSO), an anti-glutathione (GSH) compound. We demonstrate that AF potently inhibits TrxR activity and reduces the vitality and viability of HGSOC cells regardless of their sensitivities to platinum. We show that AF induces accumulation of reactive oxygen species (ROS), triggers the depolarization of the mitochondrial membrane, and kills HGSOC cells by inducing apoptosis. Yet, AF-induced cell death is abrogated by the ROS-scavenger N-acetyl cysteine (NAC). In addition, the lethality of AF is associated with the activation of caspases-3/7 and the generation of DNA damage, effects that are also prevented by the presence of NAC. Finally, when AF and L-BSO are combined, we observed a synergistic lethality against HGSOC cells, which is mediated by a further increase in ROS together with a decrease in the levels of the antioxidant GSH. In summary, our results support the concept that AF can be used alone or in combination with L-BSO to kill HGSOC cells regardless of their platinum sensitivities suggesting that depletion of antioxidants is an efficient route for treating this disease.
Image Hiding on Audio Subband Based On Centroid in Frequency Domain

ABSTRAK Audio watermarking adalah mekanisme penyembunyian data pada audio. Metode penyembunyian data yang digunakan dalam penulisan ini adalah Lifting Wavelet Transform (LWT), Fast Fourier Transform (FFT), Centroid dan Quantization Index Modulation (QIM). Langkah pertama adalah host audio tersegmentasi menjadi beberapa frame. Kemudian sub-band terpilih diubah oleh FFT dengan mengubah domain sub-band dari waktu ke frekuensi. Proses centroid digunakan untuk menemukan titik pusat frekuensi untuk lokasi penyisipan untuk mendapatkan output yang lebih stabil. Proses penyematan dilakukan dengan QIM. Kinerja watermarking oleh parameter yang disesuaikan memperoleh nilai imperceptibility dengan Signal to Noise Ratio (SNR) > 21 dB, Mean Opinion Score (MOS)> 3.8 dengan kapasitas = 86.13 bps. Selain itu, untuk sebagian besar file audio terwatermark yang diserang, metode ini tahan terhadap beberapa serangan seperti Low Pass Filter (LPF) dengan fco> 6 kHz, Band Pass Filter (BPF) dengan fco 50 Hz - 6 kHz, Linear Speed Change (LSC) dan MP4 Compression dengan Bit Error Rate (BER) kurang dari 20%. Kata kunci: FFT, subband, LWT, Centroid, Audio Watermarking, QIM ABSTRACT Audio watermarking is a mechanism for hiding data on audio. Data hiding methods used in this paper are Lifting Wavelet Transform (LWT), Fast Fourier Transform (FFT), Centroid and Quantization Index Modulation (QIM). The first step is to segment host audio into several frames, then the selected sub-band is changed by the FFT by changing the sub-band domain from time to frequency. The centroid process is used to find the center of frequency for the insertion location to get a more stable output. The embedding process is done by QIM. The watermarking performance by adjusted parameters obtains the imperceptibility value with Signal to Noise Ratio (SNR)> 21 dB, Mean Opinion Score (MOS)> 3.8 with a capacity = 86.13 bps. In addition, for most of attacked watermarked audio files, this method is resistant to several attacks such as Low Pass Filter (LPF) with fco> 6 kHz, Band Pass Filter (BPF) with fco 50 Hz - 6 kHz, Linear Speed Change (LSC) and MP4 Compression with Bit Error Rate (BER) less than 20%. Keywords: FFT, subband, LWT, Centroid, Audio Watermarking, QIM
Comparative effectiveness of pharmacological interventions for hand osteoarthritis: a systematic review and network meta-analysis of randomised trials

Objective To explore the comparative effectiveness of pharmacological interventions for hand osteoarthritis (OA). Methods We systematically searched Embase, MEDLINE, and the Cochrane Central Register of Controlled Trials from inception until 26 December 2021, for randomised trials of pharmacological interventions for people with hand OA. Two reviewers independently extracted study data and assessed the risk of bias. We calculated the effect sizes for pain (standardised mean differences) using Bayesian random effects models for network meta-analysis (NMA) and pairwise meta-analysis. Based on a pre-specified protocol, we prospectively registered the study at PROSPERO, CRD42021215393. Results We included 72 trials with 7609 participants. 65 trials (n=5957) were eligible for the quantitative synthesis, investigating 29 pharmacological interventions. Oral non-steroidal anti-inflammatory drugs (NSAIDs) and oral glucocorticoids’ NMA effect sizes were −0.18 (95% credible interval −0.36 to 0.02) and −0.54 (−0.83 to −0.24), respectively, compared with placebo, and the result was consistent when limiting evidence to the pairwise meta-analysis of trials without high risk of bias. Intra-articular hyaluronate, intra-articular glucocorticoids, hydroxychloroquine, and topical NSAIDs’ NMA effect sizes were 0.22 (−0.08 to 0.51), 0.25 (0.00 to 0.51), −0.01 (−0.19 to 0.18), and −0.14 (−0.33 to 0.08), respectively, compared with placebo. Oral NSAIDs were inferior to oral glucocorticoids with an NMA effect size of 0.36 (0.01 to 0.72). No intervention was superior to placebo when stratifying for thumb and finger OA. Conclusion Oral NSAIDs and glucocorticoids are apparently effective pharmacological interventions in hand OA. Intra-articular therapies and topical NSAIDs were not superior to placebo.
Proceedings of the ninth ACM international conference on Multimedia

Welcome to the 9th ACM Multimedia Conference, held Sept. 30-Oct. 5, 2001 in Ottawa, Ontario, the capital city of Canada. This beautiful city is often called "Silicon Valley North" because of the high concentration of major telecommunications and software companies, such as NORTEL, ALCATEL, CISCO, MITEL, COREL, COGNOS, JDS Uniphase, Entrust and many others. The conference complements this setting by presenting and exploring technological and artistic advancements in multimedia. Technical issues, theory and practice, artistic and consumer innovations will bring together researchers, artists, developers, educators, performers, and practitioners of multimedia. This conference is sponsored by NTT, ALCATEL, HP, Fuji-Xerox Palo Alto Laboratory, the Association for Computing Machinery (ACM) and its special interest groups SIGMM, SIGGRAPH, and SIGCOMM.
Electron-Impact Mass Spectrometry of PTCDA Molecules in the Gas Phase

The complete and dissociative ionizations of a 3,4,9,10-perylene-tetracarboxylic-dianhydride (C24H8O6, PTCDA) molecule in the gas phase have been studied, by using electron-impact mass spectrometry in an energy interval of 5–90 eV. The molecule is found to decay into the following fragment ions: the perylene core C20H8+ and its half C10H4+, as well as CO+, CO2+ , and O+ ions. The energy dependences of the cross-sections of the complete ionization of a PTCDA molecule and its fragment ions are analyzed. The energy of the complete ionization of a PTCDA molecule and the energies, at which its fragments appear, are determined. The temperature dependences of the formation of the most intensive fragment ions are measured, by using 80-eV electrons in a temperature interval of 320–500 K.
UvA-DARE (Digital Academic Putting things in perspective. Young people’s susceptibility to the effects of sexual media content

Research on how sexual music videos affect beliefs related to sexual aggression is rare and has not differentiated between the effects of music videos by male and female artists. Moreover, little is known about the affective processes that underlie the effects of sexual music videos. Using data from a nationally representative three-wave panel survey among 1,204 Dutch adolescents, structural equation modeling showed that viewing sexual music videos by male artists increased the acceptance of female token resistance (i.e., the notion that women say ‘no’ to sex when they actually mean ‘yes’) among adolescent girls, but not adolescent boys. Further, viewing sexual music videos by male artists influenced girls’ acceptance of token resistance indirectly via affective engagement. The findings suggest that effects of sexual music videos on stereotypical sexual beliefs depend on the specific type of music video and viewers’ gender, and can be partly explained by viewers’ affective engagement.
Economic analysis of early intervention for autistic children: findings from four case studies in England, Ireland, Italy, and Spain

Abstract Background Many autistic children experience difficulties in their communication and language skills development, with consequences for social development into adulthood, often resulting in challenges over the life-course and high economic impacts for individuals, families, and society. The Preschool Autism Communication Trial (PACT) intervention is effective in terms of improved social communication and some secondary outcomes. A previously published within-trial economic analysis found that results at 13 months did not support its cost-effectiveness. We modeled cost-effectiveness over 6 years and across four European countries. Methods Using simulation modeling, we built on economic analyses in the original trial, exploring longer-term cost-effectiveness at 6 years (in England). We adapted our model to undertake an economic analysis of PACT in Ireland, Italy, and Spain. Data on resource use were taken from the original trial and a more recent Irish observational study. Results PACT is cost-saving over time from a societal perspective, even though we confirmed that, at 13 months post-delivery, PACT is more expensive than usual treatment (across all countries) when given to preschool autistic children. After 6 years, we found that PACT has lower costs than usual treatment in terms of unpaid care provided by parents (in all countries). Also, if we consider only out-of-pocket expenses from an Irish study, PACT costs less than usual treatment. Discussion PACT may be recommended as a cost-saving early intervention for families with an autistic child.
Circinaria nimisii (Megasporaceae, lichenized Ascomycota), a new manna lichen from Greece

Abstract The manna lichens, a group of vagrant species with subfruticose and subfoliose thalli in the genus Circinaria Link, have received attention for millennia. Here, a new manna lichen species, Circinaria nimisii sp. nov. (Megasporaceae), is described and illustrated. This vagrant lichen is found on Mount Olympus in Greece and is the fourth known manna lichen in Europe. The new taxon is characterized by its subfruticose, densely-branched thallus with a muddy, earthy colour, whitish pseudocyphellae on tips of branches, mature apothecia distinctly adnate to stipitate, and paraplectenchymatous cortex tissue. Molecular sequence data from the standard barcoding marker (nrITS) also corroborate the distinction of this species from closely related congeners. Finally, Agrestia zerovii, previously known only from its type locality in Ukraine, is proposed as a new synonym of Circinaria hispida.