Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular Vesicles from PRPF31+/− iPSC-Derived RPE Have a Distinct RNA Profile Compared to Those From Healthy RPE

Retinitis pigmentosa (RP) is the most common form of inherited retinal degeneration (IRD) and causes vision loss via dysfunction and death of the photoreceptor cells and retinal pigment epithelium (RPE) of the retina. Mutations in pre-mRNA processing factor 31 (PRPF31) are associated with autosomal dominant RP, and are thought to cause retinal degeneration by causing cell autonomous defects in RPE function. Genetic therapies such as adeno-associated virus (AAV) mediated gene therapy show great promise for treating IRDs, however in many cases it is challenging to measure clinical efficacy in a timely manner because IRDs progress slowly. A potential solution to this challenge is the use of additional outcome measures, such as biomarkers. Extracellular vesicles (EVs) are lipid enclosed vesicles that are secreted by cells and their RNA contents have been proposed as potential biomarkers in cancer and other diseases. We hypothesize EV RNAs can be used as biomarkers of the health status of the neural retina and RPE. To test this hypothesis for the RPE, we used PRPF31+/+ and PRPF31+/− human induced pluripotent stem cell (hiPSC)-derived RPE to investigate the RNAs contained in RPE-derived EVs, and how they change in disease. We also compared the RNA contents of RPE-EVs with the RNAs contained in the hiPSC-RPE cells themselves. We found that EVs from mutant PRPF31+/− hiPSC-RPE cells contain distinct RNAs compared to EV from the control PRPF31+/+ hiPSC-RPE cells, suggesting EV RNA contents change during disease and can potentially serve as biomarkers of retinal degeneration.
Auditory Language Comprehension During Saccadic Eye Movements: An Investigation Using the N400 Event-Related Brain Potential

In many situations of everyday life, it is important to quickly understand a spoken message despite distraction by an already ongoing activity. Previous dual-task studies recording the N400 component of the event-related potential (ERP) have shown that auditory language comprehension can be strongly delayed by temporally overlapping additional tasks. In the current study, we investigated whether this interference is aggravated by the need for saccadic eye movements and visuospatial attention shifts in the overlapping task. In two dual-task experiments, a synonymy judgment task for spoken words was combined with a visual discrimination task at different stimulus onset asynchronies. In half of the trials, the primary visual task required a 10° exogenous saccade towards a peripheral stimulus. The timing of semantic processing in the secondary task was assessed by recording the N400. We replicated that with increasing temporal overlap between the tasks, the N400 component was strongly delayed. However, additional saccade-related processes in the primary task had no detrimental effects on concurrent spoken language processing on their own. Unexpectedly, we also observed that a preceding saccade consistently facilitated subsequent motoric processing in the visual task (as indexed by manual reaction times and the lateralized readiness potential), suggesting that saccade execution as such can significantly enhance subsequent processing.
Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site

Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. USP1, a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase I clinical trials, have been established, their binding mode is unknown. Here we use cryo-Electron Microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5 Å resolution, we discover an unusual binding mode in which the inhibitor displaces part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1. One Sentence Summary USP1, a cancer target, is inhibited by ML323 displacing part of the protein fold, allosterically disrupting the active site.
In Utero Activation of Natural Killer Cells in Congenital Cytomegalovirus Infection

Background Congenital cytomegalovirus (CMV) infection is the most common infectious cause of birth defects and neurological damage in newborns. Despite a well-established role for NK cells in control of CMV infection in older children and adults, it remains unknown whether fetal NK cells can sense and respond to CMV infection acquired in utero. Methods Here, we investigate the impact of congenital CMV infection on the neonatal NK cell repertoire by assessing the frequency, phenotype, and functional profile of NK cells in cord blood samples from newborns with congenital CMV and from uninfected controls enrolled in a birth cohort of Ugandan mothers and infants. Results We find that neonatal NK cells from congenitally CMV infected newborns show increased expression of cytotoxic mediators, signs of maturation and activation, and an expansion of mature CD56-negative NK cells, an NK cell subset associated with chronic viral infections in adults. Activation was particularly prominent in NK cell subsets expressing the Fcγ receptor CD16, indicating a role for antibody-mediated immunity against CMV in utero. Conclusion These findings demonstrate that NK cells can be activated in utero and suggest that NK cells may be an important component of the fetal and infant immune response against CMV.
Functional cell types in the mouse superior colliculus

The superior colliculus (SC) represents a major visual processing station in the mammalian brain that receives input from many types of retinal ganglion cells (RGCs). How many parallel channels exist in the SC, and what information does each encode? Here we recorded from mouse superficial SC neurons under a battery of visual stimuli including those used for classification of RGCs. An unsupervised clustering algorithm identified 24 functional types based on their visual responses. They fall into two groups: one that responds similarly to RGCs, and another with more diverse and specialized stimulus selectivity. The second group is dominant at greater depths, consistent with a vertical progression of signal processing in the SC. Cells of the same functional type tend to cluster near each other in anatomical space. Compared to the retina, the visual representation in the SC has lower dimensionality, consistent with a sifting process along the visual pathway.
Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale

Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. ABSTRACT Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
Age at cancer diagnosis by breed, weight, sex, and cancer type in a cohort of more than 3,000 dogs: Determining the optimal age to initiate cancer screening in canine patients

The goal of cancer screening is to detect disease at an early stage when treatment may be more effective. Cancer screening in dogs has relied upon annual physical examinations and routine laboratory tests, which are largely inadequate for detecting preclinical disease. With the introduction of non-invasive liquid biopsy cancer detection methods, the discussion is shifting from how to screen dogs for cancer to when to screen dogs for cancer. To address this question, we analyzed data from 3,452 cancer-diagnosed dogs to determine the age at which dogs of certain breeds and weights are typically diagnosed with cancer. In our study population, the median age at cancer diagnosis was 8.8 years, with males diagnosed at younger ages than females, and neutered dogs diagnosed at significantly later ages than intact dogs. Overall, weight was inversely correlated with age at cancer diagnosis, and purebred dogs were diagnosed at significantly younger ages than mixed-breed dogs. For breeds represented by ≥10 dogs, a breed-based median age at diagnosis was calculated. A weight-based linear regression model was developed to predict the median age at diagnosis for breeds represented by ≤10 dogs and for mixed-breed dogs. Our findings, combined with findings from previous studies which established a long duration of the preclinical phase of cancer development in dogs, suggest that it might be reasonable to consider annual cancer screening starting 2 years prior to the median age at cancer diagnosis for dogs of similar breed or weight. This logic would support a general recommendation to start cancer screening for all dogs at the age of 7, and as early as age 4 for breeds with a lower median age at cancer diagnosis, in order to increase the likelihood of early detection and treatment.
Molecular-dynamics simulation methods for macromolecular crystallography

To assess the potential benefits of molecular-dynamics (MD) simulations for macromolecular crystallography (MX), we performed room-temperature X-ray diffraction studies of the catalytic subunit of mouse protein kinase A (PKA-C). We then performed crystalline MD simulations of PKA-C, computed simulated electron densities from the water, protein, and ion components of the MD simulations, and carefully compared them to the initial crystal structure. The results led to the development of an MD-MX analysis procedure and several associated methods: 1) density comparison to evaluate consistency between the MD and the initial crystal structure model; 2) water building to generate alternative solvent models; and 3) protein remodeling to improve the crystal structure where interpretation of density is unclear. This procedure produced a revised structure of PKA with a new ordered water model and a modified protein structure. The revisions yield new insights into PKA mechanisms, including: a sensitivity of the His294 conformation to protonation state, with potential consequences for regulation of substrate binding; a remodeling of the Lys217 side chain along with a bound phosphate; an alternative conformation for Lys213 associated with binding to the regulatory subunit; and an alternative conformation for catalytic base Asp166 and nearby waters, suggesting a mechanism of progression of the phosphotransfer reaction via changes in Mg2+ coordination. Based on the benefits seen applying these methods to PKA, we recommend incorporating our MD-MX procedure into MX studies, to decide among ambiguous interpretations of electron density that occur, inevitably, as part of standard model refinement.
Functional coupling of the mesencephalic locomotor region and V2a reticulospinal neurons driving forward locomotion

Locomotion in vertebrates relies on high brain centers converging onto the mesencephalic locomotor region (MLR). How the MLR recruits brainstem reticulospinal neurons (RSNs) to initiate locomotion is incompletely understood due to the challenge of recording these cells in vivo. To tackle this question, we leveraged the transparency and genetic accessibility of larval zebrafish. In this model organism, we uncovered the locus of the MLR as a small region dorsal to the locus coeruleus containing glutamatergic and cholinergic neurons. MLR stimulations reliably elicited forward bouts of controlled duration and speed. We find that the MLR elicits forward locomotion by recruiting V2a RSNs in the pontine and retropontine regions, and gradually in the medulla. Remarkably, recruited V2a RSNs in the medulla act as maintain cells encoding speed of forward locomotion. Altogether, our study reveals that the MLR recruits genetically-identified reticulospinal neurons in the medulla to control the kinematics of exploration.
Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes

High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
Use of biomass in the iron and steel industry - An Australian perspective

Since late-2006, in response to climate change, BlueScope Steel and OneSteel, partnering with CSIRO, have conducted an RD cokemaking blend component; steelmaking recarburiser; and, in the blast furnace, as a tuyere injectant (the largest application), nut coke replacement and reductant for pre-reduced feeds. For the EAF route, applications include replacement for charge carbon, foaming agent and steel recarburiser. Work has included several life- cycle and techno-economic studies as well as technology reviews. In all of the applications studied it has been found that charcoal properties can be usefully optimised, thus a concept referred to as "designer char" has been developed. In this paper, brief mention will be made of several applications, but emphasis has been placed on theoretical, economic and combustion studies of charcoal types considered for blast furnace tuyere injection.
High Mobility Group Box-1 and Diabetes Mellitus Complications: State of the Art and Future Perspectives

Diabetes mellitus (DM) is an endemic disease, with growing health and social costs. The complications of diabetes can affect potentially all parts of the human body, from the heart to the kidneys, peripheral and central nervous system, and the vascular bed. Although many mechanisms have been studied, not all players responsible for these complications have been defined yet. High Mobility Group Box-1 (HMGB1) is a non-histone nuclear protein that has been implicated in many pathological processes, from sepsis to ischemia. The purpose of this review is to take stock of all the most recent data available on the role of HMGB1 in the complications of DM.
Melt-Mixed 3D Hierarchical Graphene/Polypropylene Nanocomposites with Low Electrical Percolation Threshold

Graphene-based materials are a family of carbonaceous structures that can be produced using a variety of processes either from graphite or other precursors. These materials are typically a few layered sheets of graphene in the form of platelets and maintain some of the properties of pristine graphene (such as two-dimensional platelet shape, aspect ratio, and graphitic bonding). In this work we present melt mixed graphene-based polypropylene systems with significantly reduced percolation threshold. Traditionally melt-mixed systems suffer from poor dispersion that leads to high electrical percolation values. In contrast in our work, graphene was added into an isotactic polypropylene matrix, achieving an electrical percolation threshold of ~1 wt. %. This indicates that the filler dispersion process has been highly efficient, something that leads to the suppression of the β phase that have a strong influence on the crystallization behavior and subsequent thermal and mechanical performance. The electrical percolation values obtained are comparable with reported solution mixed systems, despite the use of simple melt mixing protocols and the lack of any pre or post-treatment of the final compositions. The latter is of particular importance as the preparation method used in this work is industrially relevant and is readily scalable.
Markets and Morality: How Markets Shape Our (Dis)Regard for Others

Competing Interest Statement : The authors have no competing interests pertaining to this research. Abstract Theorists since David Hume and Adam Smith have debated possible causal connections between economic market experiences and “moral sentiments”––that is, beliefs concerning what constitutes right and wrong, and the nature of one’s responsibilities to others. Some have hypothesized that participation in market competition may encourage an increasing prioritization of self-interest over social responsibilities to others while other theorists have proposed that competitive markets may foster greater altruism, mutual understanding, and broader social ties through the disruption of geographical and tribal isolation––what eighteenth-century political philosophers called the doux commerce thesis. We use an international experimental design to evaluate this thesis by measuring the impact of market interactions on utilitarian versus deontological values, others-regarding preferences, and charitable donations. Through a labor-market intermediary, we randomly assign workers to diﬀerent market conditions: competitive (tourna-ment) or commodifying (piece-rate). We ﬁnd that in contexts with lower levels of income, competition increases others-regarding preferences, deontological commitments towards out-group members, productivity, and charitable donations by productive workers (but decreases donations by less productive workers). In contexts with higher levels of income, these eﬀects ﬂip: competition decreases others-regarding preferences and decreases deontological commitments as utilitarian principles of maximization assume greater prominence in decision-making. The eﬀect of competition on deontological commitments to others thus reverses with increasing income. In light of growing economic inequality and reduced social cohesion observed in many wealthy nations today, our ﬁndings suggest a greater need for market regulation at higher levels of income to counteract the corrosion of social relations by unmitigated market forces. at higher levels of income, competition increases self-interested behavior. Our ﬁndings suggest that market regulation becomes more important for protecting social cohesion and interpersonal responsibility as income levels increase. A runaway trolley is hurtling down the tracks toward ﬁve people who will be killed if it proceeds on its present course. You are standing next to a large man on a footbridge spanning the tracks. The only way to save the ﬁve people is to push the man oﬀ the footbridge and into the path of the trolley , but if you do that, the large man will be killed. Is it morally permissible to push the man oﬀ the bridge?