Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Mental Health and Addiction Service use Prior to and During Incarceration in Provincial Jails in Ontario, Canada: A Retrospective Cohort Study

Objective Individuals with mental illness and addiction are overrepresented in prisons. Few studies have assessed mental health and addiction (MHA)-related service use among individuals experiencing incarceration using health administrative data and most focus on service use after prison release. The objective of this study was to determine the prevalence of MHA-related service use in the 5 years prior to and during incarceration. Methods We used linked correctional and administrative health data for people released from Ontario provincial jails in 2010. MHA-related service use in the 5 years prior to the index incarceration was categorized hierarchically into four mutually exclusive categories based on the type of service use: psychiatric hospitalization, MHA-related emergency department (ED) visit, MHA-related outpatient visit (from psychiatrist or primary care physician), and no MHA-related service use. Demographic, diagnostic, and incarceration characteristics were compared across the four service use categories. MHA-related service use during the index incarceration was assessed by category and length of incarceration. Results A total of 48,917 individuals were included. Prior to incarceration, 6,116 (12.5%) had a psychiatric hospitalization, 8,837 (18.1%) had an MHA-related ED visit, and 15,866 (32.4%) had an MHA-related outpatient visit. Of the individuals with any MHA-related service prior to incarceration, 60.4% did not receive outpatient care from a psychiatrist prior to incarceration and 65.6% did not receive MHA-related care during incarceration. Conclusion Despite a high prevalence of mental illness and addiction among people experiencing incarceration, access to and use of MHA-related care prior to and during incarceration is poor. Increasing the accessibility and use of MHA-related services throughout the criminal justice pathway is warranted.
Global water availability and its distribution under the Coupled Model Intercomparison Project Phase Six scenarios

Changes in the hydrological cycle have widespread consequences and remain uncertain under climate change. We analyse the changes in major water components of the hydrological cycle, that is, precipitation (P), runoff (Q), evapotranspiration (E), precipitation minus evapotranspiration (P − E), and terrestrial water storage (S), and quantify the uncertainties across the 21st century with Phase Six of the Coupled Model Intercomparison Project (CMIP6) simulations. The multimodel ensemble based on over 10 GCMs shows that P − E and Q share similar trends with P, with increases expected in northern high latitudes of Eurasia and North America, South Asia, and eastern Africa, and decreases expected in Central America, the Mediterranean, and the Amazon. The seasonal changes in S at mid and high latitudes are behind the large seasonal shifts in Q while changes in P − E are dominantly affected by P. The equatorial regions are expected to have the largest changes and intermodel variability. From low emission scenario SSP1‐2.6 to high emission scenario SSP5‐8.5, the spatial patterns for future changes remain consistent while more drastic and more widespread changes are expected globally over time with warming for all water components. Larger intermodel variability is also found under higher emission scenarios. The study provides a comprehensive perspective on the assessment of annual and seasonal changes in all water components within the hydrological cycle as well as the associated uncertainty with the latest CMIP6 simulations under three representative scenarios, providing the most updated climate information for formulating appropriate mitigation and adaptation.
Complex aneuploidy triggers autophagy and p53-mediated apoptosis and impairs the second lineage segregation in human preimplantation embryos

About 70% of human cleavage stage embryos show chromosomal mosaicism, falling to 20% in blastocysts. Chromosomally mosaic human blastocysts can implant and lead to healthy new-borns with normal karyotypes. Studies in mouse embryos and human gastruloids have shown that aneuploid cells show proteotoxic stress, autophagy and p53 activation and that they are eliminated from the epiblast by apoptosis while being rather tolerated in the trophectoderm. These observations suggest a selective loss of aneuploid cells from human embryos, but the underlying mechanisms are not yet fully understood. In this study we investigated the cellular consequences of aneuploidy in a total of 85 human blastocysts. RNA-sequencing of trophectoderm cells showed transcriptional signatures of a deregulated p53 pathway and apoptosis, which was proportionate to the level of chromosomal imbalance. Immunostaining revealed that aneuploidy triggers proteotoxic stress, autophagy and apoptosis in aneuploid embryos. Total cell numbers were lower in aneuploid embryos, due to a decline both in trophectoderm and in epiblast/primitive endoderm cell numbers. While lower cell numbers in trophectoderm may be attributed to apoptosis, it appeared that aneuploidy impairs the second lineage segregation and primitive endoderm formation in particular. Our findings might explain why fully aneuploid embryos fail to further develop and we hypothesize that the same mechanisms lead to removal of aneuploid cells from mosaic embryos. This hypothesis needs further study as we did not analyse chromosomal mosaic embryos. Finally, we demonstrated clear differences with previous findings in the mouse, emphasizing the need for human embryo research to understand the consequences of aneuploidy.
Negative allosteric modulation of the glucagon receptor by RAMP2

Receptor activity-modifying proteins (RAMPs) modulate the activity of many Family B heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs). The glucagon receptor (GCGR), a Family B GPCR responsible for maintenance of proper blood sugar levels, interacts with RAMP2, though the purpose and consequence of this interaction is poorly understood. Using a series of biochemical and cell-based assays, we show that RAMP2 interacts with and broadly inhibits GCGR-induced downstream signaling. Hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) demonstrates that RAMP2 enhances local flexibility in select locations in and near the receptor extracellular domain (ECD) as well as at a key region in the 6th transmembrane helix, while single-molecule fluorescence resonance energy transfer (smFRET) experiments show that this RAMP2-induced ECD disorder results in inhibition of active and intermediate states of the intracellular face of the receptor. Using cryo-electron microscopy (cryoEM), we determined the structure of the GCGR-Gs complex at 2.9 Å resolution in the presence of RAMP2. RAMP2 apparently does not interact with GCGR in an ordered manner, yet the ECD of GCGR is indeed largely disordered in the presence of RAMP2. This disorder is accompanied by rearrangements of several key areas of the receptor, resulting in the formation of a likely unproductive complex. Together, our studies suggest that RAMP2 acts as a negative allosteric modulator of GCGR by enhancing conformational sampling of the ECD.
General cognitive performance declines with female age and is negatively related to fledging success in a wild bird

Identifying the causes and fitness consequences of intraspecific variation in cognitive performance is fundamental to understand how cognition evolves. Selection may act on different cognitive traits separately or jointly as part of the general cognitive performance of the individual. To date, few studies have examined simultaneously whether individual cognitive performance covaries across different cognitive tasks, the relative importance of individual and social attributes in determining cognitive variation, and its fitness consequences in the wild. Here, we tested 38 wild southern pied babblers (Turdoides bicolor) on a cognitive test battery targeting associative learning, reversal learning and inhibitory control. We found that a single factor explained 59.5% of the variation in individual cognitive performance across tasks, suggestive of a general cognitive factor. General cognitive performance varied by age and sex; declining with age in females but not males. Older females also tended to produce a higher average number of fledglings per year compared to younger females. Analysing over 10 years of breeding data, we found that individuals with lower general cognitive performance produced more fledglings per year. Collectively, our findings support the existence of a trade-off between cognitive performance and reproductive success in a wild bird.
Nuclear-enriched protein phosphatase 4 ensures outer kinetochore assembly prior to nuclear dissolution

A landmark event in the transition from interphase to mitosis in metazoans is nuclear envelope breakdown (NEBD). Many events important for mitosis occur prior to NEBD, including condensation of replicated chromosomes and assembly of kinetochores to rapidly engage spindle microtubules. Here we show that nuclear-enriched protein phosphatase 4 (PP4) ensures robust assembly of the microtubule-coupling outer kinetochore prior to NEBD. In the absence of PP4, chromosomes exhibit extended monopolar orientation after NEBD and subsequently mis-segregate. A secondary consequence of diminished outer kinetochore assembly is defective sister chromatid resolution. After NEBD, a cytoplasmic activity compensates for PP4 loss, leading to outer kinetochore assembly and recovery of chromosomes from monopolar orientation to significant biorientation. The Ndc80-Ska microtubule-binding module of the outer kinetochore is required for this recovery. PP4 associates with the inner kinetochore protein CENP-C; however, disrupting the PP4–CENP-C interaction does not perturb chromosome segregation. These results establish that PP4-dependent outer kinetochore assembly prior to NEBD is critical for timely and proper engagement of chromosomes with spindle microtubules.
Prevalence and genetic characterisation of Giardia duodenalis in river water and riverbed sediment using next-generation sequencing

Giardia duodenalis has been reported in different sources such as water, human stools, animal stools, vegetable farms and markets and soil of public places. However, different assemblages of G.duodenalis harboured in riverbed sediments have not yet been investigated. Thus, in this study, we quantified and genetically characterised G.duodenalis harboured in the water column and the riverbed sediment of the Apies River to cross this frontier of the unknown in freshwater sediment. Enumeration of G.duodenalis cysts was performed by epifluorescence microscopy observation and quantitative polymerase chain reaction (qPCR). Genetic characterisation was achieved by next-generation sequencing (NGS) using the β-giardin gene and bioinformatics analysis of the NGS data. Results obtained through epifluorescence microscopy revealed a prevalence rate of 87% (140/160) of G.duodenalis cysts in river water, which was higher than that observed in riverbed sediments (78%, 125/160). However, the qPCR assay showed that gene copies of G.duodenalis, which ranged between3.27 log10 and 7.26 log10 copies/L in re-suspended riverbed sediments, and between 0.49 log10 and 3.95 log10 copies/L in river water Genetic characterisation revealed six and seven assemblages in river water (A, B, C, D, E and F) and riverbed sediment (A, B, C, D, E, F and G), respectively. Both matrices carried similar sub-assemblages belonging to assemblages A (AI, AII and AIII) and B (BI, BII, BIII, BIV and BV), whereas riverbed sediment carried an additional sub-assemblage BX belonging to the assemblage B. The present genetic characterisation results suggest that Apies River water and its bed sediment harbour considerable quantities of G.duodenalis cysts that may cause infections in humans and animals if ingested. Consequently, monitoring of both the water column and respective bed sediments for the presence of G.duodenalis is justified to develop strategies for the protection of public health. This study also calls for urgent identification of point sources that are responsible for the contamination of this freshwater source and its sediment. Author summary
Adaptation of Dynamics in Default Mode Network Depending on Mental States: the One-to-many dynamic functional connectivity analysis with fMRI Adaptation in dynamics of local brain network

We suggest a novel analysis method called the one-to-many dynamic functional connectivity analysis to detect the adaptation of dynamics in a local brain network depending on mental states with a single case study. We collected fMRI BOLD signals from a blind subject whom with advanced ability in episodic memory retrieval while the subject was resting and retrieving a morning routine which is a type of autobiographical episodic memory. The default mode network is known for its high activation in these mental states. By applying the principal components analysis to the partial correlations of a brain region in the default mode network, which are correlations of the brain region to the rest of the network, we compared how congruent first or second principal components of the partial correlations of the brain region the default mode network in the two mental states. Our results showed that the adaption of the dynamics in the default mode network in the two mental states could be well depicted when the partial correlations of the posterior cingulate cortex are considered. Specifically, the correlation of the posterior cingulate cortex and the right parahippocampal cortex contributed mostly to the adaptation of the partial correlations of the posterior cingulate cortex for this single subject case.
Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture

The dynamics of inheritance of histones and their associated modifications across cell divisions can have major consequences on maintenance of the cellular epigenomic state. Recent experiments contradict the long-held notion that histone inheritance during replication is always local, suggesting that active and repressed regions of the genome exhibit fundamentally different histone dynamics independent of transcription-coupled turnover. Here we develop a stochastic model of histone dynamics at the replication fork and demonstrate that differential diffusivity of histones in active versus repressed chromatin is sufficient to quantitatively explain these recent experiments. Further, we use the model to predict patterns in histone mark similarity between pairs of genomic loci that should be developed as a result of diffusion, but not from PRC2 mediated mark spreading or transcriptional processes. Interestingly, using a combination of CHIP-seq, replication timing and Hi-C datasets we demonstrate that all the computationally predicted patterns are consistently observed for both active and repressive histone marks in two different cell lines. Our results suggest that in contrast to current models that posit histone transfer exclusively between parental and daughter DNA strands, dislodged histones in euchromatin and facultative heterochromatin diffuse within larger “Diffusion-Accessible-Domains” (DADs), leading to redistribution of epigenetic marks both within and across chromosomes. Preservation of the epigenomic state across cell divisions therefore might be achieved not by passing on strict positional information of histone marks, but by maintaining the marks in somewhat larger DADs of the genome.
In situ imaging across ecosystems to resolve the fine-scale oceanographic drivers of a globally significant planktonic grazer

Doliolids are common gelatinous grazers in marine ecosystems around the world and likely influence carbon cycling due to their large population sizes with high growth and excretion rates. Aggregations or blooms of these organisms occur frequently, but they are difficult to measure or predict because doliolids are fragile, under sampled with conventional plankton nets, and can aggregate on fine spatial scales (1-10 m). Moreover, ecological studies typically target a single region or site that does not encompass the range of possible habitats favoring doliolid proliferation. To address these limitations, we combined in situ imaging data from six coastal ecosystems, including the Oregon shelf, northern California, southern California Bight, northern Gulf of Mexico, Straits of Florida, and Mediterranean Sea, to resolve and compare doliolid habitat associations during warm months when environmental gradients are strong and doliolid blooms are frequently documented. Higher ocean temperature was the strongest predictor of elevated doliolid abundances across ecosystems, with additional variance explained by chlorophyll-a fluorescence and dissolved oxygen. For marginal seas with a wide range of productivity regimes, the nurse stage tended to comprise a higher proportion of the doliolids when total abundance was low. However, this pattern did not hold in ecosystems with persistent coastal upwelling. The doliolids tended to be most aggregated in oligotrophic systems (Mediterranean and southern California), suggesting that microhabitats within the water column favor proliferation on fine spatial scales. Similar comparative approaches can resolve the realized niche of fast-reproducing marine animals, thus improving predictions for population-level responses to changing oceanographic conditions.
Nucleotide and structural polymorphisms of the eastern oyster genome paint a mosaic of divergence, selection, and human impacts

The eastern oyster, Crassostrea virginica, is a valuable fishery and aquaculture species that provides critical services as an ecosystem engineer. Oysters have a life-history that promotes high genetic diversity and gene flow while also occupying a wide range of habitats in variable coastal environments from the southern Gulf of Mexico to the southern waters of Atlantic Canada. To understand the interplay of genetic diversity, gene flow, and intense environmental selection, we used whole genome re-sequencing data from 90 individuals across the eastern United States and Gulf of Mexico, plus 5 selectively bred lines. Our data confirmed a large phylogeographic break between oyster populations in the Gulf of Mexico and the Atlantic coast of the USA. We also demonstrated that domestication has artificially admixed genetic material between the two ocean basins, and selected lines with admixed ancestry continue to maintain heterozygosity at these sites through several generations post admixture, possibly indicating relevance to desirable aquaculture traits. We found that genetic and structural variation are high in both wild and selected populations, but we also demonstrated that, when controlling for domestication admixture across ocean basins, wild populations do have significantly higher levels of nucleotide diversity and copy number variation than selected lines. Within the Atlantic coast, we detected subtle but distinct population structure, introgression of selected lines within wild individuals, an interaction between structural variation and putatively adaptive population structure, and evidence of candidate genes responding to selection from salinity. Our study highlights the potential for applying whole genome sequencing to highly polymorphic species and provides a road map for future work examining the genome variation of eastern oyster populations.
Oculomotor and neural correlates of semantic and morphological priming in natural sentence reading

Our current understanding of visual word identification is difficult to extend to text reading–both experiments and theories focus primarily, if not exclusively, on out–of–context individual words. Here, we try to fill this gap by studying cross–word semantic and morphological priming within sentences in natural reading, in a novel coregistration paradigm with simultaneous recording of eye movements and electroencephalography. We report results from both eye tracking measures, and, more importantly, from Fixation-Related potentials, time-locked to the fixation onset on the target word. In both, semantic facilitation clearly emerged, while we observed no effect of morphological priming. These results may indicate that morphological agreement is at least partially computed outside of the lexical-semantic system which gives rise to semantic priming. These results provide new insight into the neural correlates of semantic and morphological priming in natural reading, revealing lexical dynamics as they likely emerge in our everyday reading experience.
Environmental DNA phylogeography: successful reconstruction of phylogeographic patterns of multiple fish species from a cup of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionise phylogeography.