Dual pathogenicity island transfer by piggybacking lateral transduction.

Lateral transduction (LT) is the process by which temperate phages mobilize large sections of bacterial genomes. Despite its importance, LT has only been observed during prophage induction. Here, we report that superantigen-carrying staphylococcal pathogenicity islands (SaPIs) employ a related but more versatile and complex mechanism of gene transfer to drive chromosomal hypermobility while self-transferring with additional virulence genes from the host. We found that after phage infection or prophage induction, activated SaPIs form concatamers in the bacterial chromosome by switching between parallel genomic tracks in replication bubbles. This dynamic life cycle enables SaPIbov1 to piggyback its LT of staphylococcal pathogenicity island vSaα, which encodes an array of genes involved in host-pathogen interactions, allowing both islands to be mobilized intact and transferred in a single infective particle. Our findings highlight previously unknown roles of pathogenicity islands in bacterial virulence and show that their evolutionary impact extends beyond the genes they carry.

Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion.

The use of long-read direct RNA sequencing (DRS) and PCR cDNA sequencing (PCS) in clinical oncology remains limited, with no direct comparison between the two methods. We used DRS and PCS to study clear cell renal cell carcinoma (ccRCC), focussing on new transcript and gene discovery. Twelve primary ccRCC archival tumors, six from patients who went on to relapse, were analysed. Results were validated in an independent cohort of twenty patients by qRT-PCR and compared to DRS analysis of RCC4 cells. In archival clinical samples and due to long-term storage, average read length was lower (400-500nt) than that achieved through DRS of RCC4 cells (>1100nt). Still, deconvolution analysis showed a loss of immune infiltrate in primary tumors of patients who relapse as reported by others. Differentially expressed genes in patients who went on to relapse were determined with good overlap between DRS and PCS, identifying LINC04216 and the T cell exhaustion marker TOX as novel candidate recurrence-associated genes. Novel transcript analysis revealed over 10,000 candidate novel transcripts detected by both methods and in ccRCC cells in vitro, including a novel CD274 (PD-L1) transcript encoding for the soluble version of the protein with a longer 3' UTR and lower stability than the annotated transcript. Both methods identified 414 novel genes, also detected in RCC4 cells, including a novel noncoding gene over-expressed in patients who relapse. Overall, we showcase use of PCS and DRS in archival tumor samples to uncover unmapped features of cancer transcriptomes, linked to disease progression and immune evasion.

Sex differences in trajectories of cortical development in autistic children from 2-13 years of age.

Previous studies have reported alterations in cortical thickness in autism. However, few have included enough autistic females to determine if there are sex specific differences in cortical structure in autism. This longitudinal study aimed to investigate autistic sex differences in cortical thickness and trajectory of cortical thinning across childhood. Participants included 290 autistic (88 females) and 139 nonautistic (60 females) individuals assessed at up to 4 timepoints spanning ~2-13 years of age (918 total MRI timepoints). Estimates of cortical thickness in early and late childhood as well as the trajectory of cortical thinning were modeled using spatiotemporal linear mixed effects models of age-by-sex-by-diagnosis. Additionally, the spatial correspondence between cortical maps of sex-by-diagnosis differences and neurotypical sex differences were evaluated. Relative to their nonautistic peers, autistic females had more extensive cortical differences than autistic males. These differences involved multiple functional networks, and were mainly characterized by thicker cortex at ~3 years of age and faster cortical thinning in autistic females. Cortical regions in which autistic alterations were different between the sexes significantly overlapped with regions that differed by sex in neurotypical development. Autistic females and males demonstrated some shared differences in cortical thickness and rate of cortical thinning across childhood relative to their nonautistic peers, however these areas were relatively small compared to the widespread differences observed across the sexes. These results support evidence of sex-specific neurobiology in autism and suggest that processes that regulate sex differentiation in the neurotypical brain contribute to sex differences in the etiology of autism.

Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock.

Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.

Biphasic burrowing in Atlantic hagfish (Myxine limosa).

Myxine limosa is a burrowing species of hagfish that occurs in the western North Atlantic in areas with muddy substrate and at depths generally greater than 100 meters. Burrowing of M. limosa has been observed from submersibles, but little is known about the behavior of these animals within the substrate or the biomechanical mechanisms involved. Here, we investigated burrowing in M. limosa by observing individuals as they burrowed through transparent gelatin. A photoelastic setup using crossed polarizers allowed us to visualize stress development in the gelatin as the hagfish moved through it. We found that M. limosa created U-shaped burrows in gelatin using a stereotyped, two-phase burrowing behavior. In the first ('thrash') phase, hagfish drove their head and their anterior body into the substrate using vigorous sinusoidal swimming movements, with their head moving side-to-side. In the second ('wriggle') phase, swimming movements ceased, with propulsion coming exclusively from the anterior, submerged portion of body. The wriggle phase involved side-to-side head movements and movements of the submerged part of the body that resembled the internal concertina strategy used by caecilians and uropeltid snakes. The entire burrowing process took on average 7.6 min to complete and ended with the hagfish's head protruding from the substrate and the rest of its body generally concealed. Understanding the burrowing activities of hagfishes could lead to improved understanding of sediment turnover in marine benthic habitats, new insights into the reproductive behavior of hagfishes, or even inspiration for the design of burrowing robots.

Diffusional and Biochemical Limitations to Photosynthesis Under Water Deficit for Field-Grown Cotton.

Water deficit stress limits net photosynthetic rate (AN), but the relative sensitivities of underlying processes such as thylakoid reactions, ATP production, carbon fixation reactions, and carbon loss processes to water deficit stress in field-grown upland cotton require further exploration. Therefore, the objective of the present study was to assess (1) the diffusional and biochemical mechanisms associated with water deficit-induced declines in AN and (2) associations between water deficit-induced variation in oxidative stress and energy dissipation for field-grown cotton. Water deficit stress was imposed for three weeks during the peak bloom stage of cotton development, causing significant reductions in leaf water potential and AN. Among diffusional limitations, mesophyll conductance was the major contributor to the AN decline. Several biochemical processes were adversely impacted by water deficit. Among these, electron transport rate and RuBP regeneration were most sensitive to AN-limiting water deficit. Carbon loss processes (photorespiration and dark respiration) were less sensitive than carbon assimilation, contributing to the water deficit-induced declines in AN. Increased energy dissipation via non-photochemical quenching or maintenance of electron flux to photorespiration prevented oxidative stress. Declines in AN were not associated with water deficit-induced variation in ATP production. It was concluded that diffusional limitations followed by biochemical limitations (ETR and RuBP regeneration) contributed to declines in AN, carbon loss processes partially contributed to the decline in AN, and increased energy dissipation prevented oxidative stress under water deficit in field-grown cotton.

A widespread family of WYL-domain transcriptional regulators co-localizes with diverse phage defence systems and islands.

Bacteria are under constant assault by bacteriophages and other mobile genetic elements. As a result, bacteria have evolved a multitude of systems that protect from attack. Genes encoding bacterial defence mechanisms can be clustered into 'defence islands', providing a potentially synergistic level of protection against a wider range of assailants. However, there is a comparative paucity of information on how expression of these defence systems is controlled. Here, we functionally characterize a transcriptional regulator, BrxR, encoded within a recently described phage defence island from a multidrug resistant plasmid of the emerging pathogen Escherichia fergusonii. Using a combination of reporters and electrophoretic mobility shift assays, we discovered that BrxR acts as a repressor. We present the structure of BrxR to 2.15 Å, the first structure of this family of transcription factors, and pinpoint a likely binding site for ligands within the WYL-domain. Bioinformatic analyses demonstrated that BrxR-family homologues are widespread amongst bacteria. About half (48%) of identified BrxR homologues were co-localized with a diverse array of known phage defence systems, either alone or clustered into defence islands. BrxR is a novel regulator that reveals a common mechanism for controlling the expression of the bacterial phage defence arsenal.

Cohort study on immune checkpoint inhibitor-associated acute kidney injury: Incidence, risk factors, and management strategies.

INTRODUCTION: Case studies and retrospective chart reviews of health system data have demonstrated an increased risk of nephrotoxicity in patients receiving immune checkpoint inhibitors compared to clinical trials. This study investigated the frequency, causes, and risk factors for acute kidney injury in a real-world, rural setting. METHODS: This was a retrospective cohort study of patients who received at least one dose of a checkpoint inhibitor at a rural health system from May 2013 to February 2020 and who received at least one dose of a checkpoint inhibitor. Electronic and manual chart review helped to determine the incidence of, risk factors for, and renal outcomes and management strategies of checkpoint inhibitor-related acute kidney injury. Multivariable Fine and Gray subdistribution hazard models were used to assess the impact of patient characteristics on the incidence of sustained acute kidney injury and checkpoint inhibitor-induced acute kidney injury. RESULTS: After exclusion criteria, 906 patients who received at least one dose of a checkpoint inhibitor at Marshfield Clinic Health System during the study period were included. The incidence of acute kidney injury of any duration and due to any cause was 36.1%, while sustained acute kidney injury occurred in 28.7% of patients. Checkpoint inhibitor-related acute kidney injury was thought to have occurred in 2.7% of patients. Baseline estimated glomerular filtration rate < 60 was the sole predictor of checkpoint inhibitors-related acute kidney injury. Most patients with suspected checkpoint inhibitor-related acute kidney injury were managed with corticosteroids, and 62.5% experienced complete renal recovery. CONCLUSIONS: Ours is the first retrospective cohort study to test whether baseline Eastern Cooperative Oncology Group score and checkpoint inhibitor place in therapy were associated with checkpoint inhibitor-related acute kidney injury, and neither of these data points were found to be predictive. Even after expanding the parameters and methodologies of our study as compared to other retrospective cohort studies, we found only three baseline characteristics to be predictive of sustained acute kidney injury: Baseline eGFR, loop diuretic, and spironolactone use. For checkpoint inhibitor-related baseline, eGFR alone was predictive.

Measuring and improving quality in esophageal care and swallowing disorders.

Evaluating clinical care through quality-related metrics is increasingly common. There are now numerous quality statements and indicators related to the medical management of benign and pre-malignant esophageal diseases. Expert consensus leveraging evidence-based recommendations from published society guidelines has been the most frequently used basis for developing esophageal quality statements. While surgical care of patients with esophageal malignancies, including squamous cell carcinoma, has also been developed, those related to benign esophageal disease now include domains of diagnosis, treatment, and monitoring for gastroesophageal reflux disease, eosinophilic esophagitis (EoE), achalasia, and Barrett's esophagus (BE). Several recent studies evaluating adherence to quality metrics affirm substantial variation in practice patterns with opportunities for improvement in care across esophageal diseases. In particular, patient education regarding treatment options in achalasia, frequency of esophageal biopsies among patients with dysphagia to evaluate for EoE, and endoscopic evaluation within a BE segment are areas identified to have need for improvement. As the management of esophageal diseases becomes more complex and interdisciplinary, adherence to quality metrics may be a source of standardization and improvement in delivery and ultimately patient outcomes. Indeed, the development of national quality databases has resulted in a significant growth in the use of these metrics for quality improvement activities and may form the basis for future inclusion in quality reporting and payment programs.

Experiences and access of palliative and end of life care for older people from minority ethnic groups: a scoping review.

BACKGROUND: Many older people from minority ethnic groups experience inequalities towards the end of life, including barriers to accessing palliative care. With levels of international migration increasing, there is a need to understand these differences and consider the needs of minority ethnic groups in healthcare policies. This review aimed to map evidence on how older people from minority ethnic groups access and utilise palliative and end of life care, preferences for palliative and end of life care, experiences of palliative and end of life care, and how this varies between minority ethnic groups in different countries, and with different health conditions. METHODS: Scoping review, following Joanna Briggs Institute (JBI) guidance. Searches of eight online databases (MEDLINE, Embase, Web of Science, CINAHL, PsycInfo, Assia, Scopus, and the Cochrane Library) and grey literature were undertaken in 2024. Qualitative sources that focused on older people from minority ethnic groups' and carers' access to and use of palliative and end of life care were included, as well as those focusing on healthcare professionals' experiences. RESULTS: Twenty-three sources were included in the review, the majority of which were interview studies from the USA. Findings reflect a range of preferences, inequalities, facilitators and barriers to accessing palliative and end of life care, with themes relating to: (1) Knowledge of hospice and palliative care, (2) societal and structural issues, (3) language and health literacy, (4) migratory experiences, (5) trust in healthcare services and professionals, (6) religion and hope, and (7) cultural values. CONCLUSIONS: This review identified areas for healthcare providers to consider developing more culturally appropriate palliative and end of life care practice, including building trust and improving communication, sharing information, reducing language barriers, addressing stigma, and, if relevant, acknowledging the importance of culture and religion. Further qualitative research from an intersectional perspective, such as geographical location or socio-economic status, rather than race, ethnicity, and culture alone, is needed in more diverse geographical settings and on specific health conditions.

Provider and administrator attitudes and experiences with implementing telebuprenorphine during the COVID-19 pandemic: a mixed-methods survey.

Introduction: This mixed-methods study assessed buprenorphine provider and administrator perceptions and experiences in offering telebuprenorphine during the COVID-19 pandemic. Methods: Semi-structured interviews were conducted between June 2021 and September 2021 among telebuprenorphine providers and administrators (N=16) and assessed for program design and implementation strategies, clinical workflow, patient-level factors influencing program entry and retention, and challenges and solutions to improving clinical care. Results: Clinician (n=15) and administrator (n=1) participants identified changes to clinical workflow, including increased administrative tasks to confirm patient receipt of prescribed medications, completion of referrals to community- or specialty treatment, and locating available pharmacies and laboratory services. Challenges consisted of staff redeployment to COVID-19 related responsibilities, prior authorization requirements for buprenorphine prescriptions, billing structures that under-reimbursed for telephone or video visits, and concerns with changes in government regulations. Strategies to improving telebuprenorphine included offering "hotlines" to facilitate same-day visits, expanding between-visit support, establishing workflows with community pharmacies to ensure seamless dispensing of buprenorphine, co-location of behavioral health providers, and distributing donated mobile phones to patients. Suggested technologies for enhancing care included text messaging (75%) and smartphone applications (56.3%). Conclusions: Findings from this study highlight considerable heterogeneity in the delivery of telebuprenorphine services.

Altered Development of Amygdala-Connected Brain Regions in Males and Females with Autism.

Altered amygdala development is implicated in the neurobiology of autism, but little is known about the coordinated development of the brain regions directly connected with the amygdala. Here we investigated the volumetric development of an amygdala-connected network, defined as the set of brain regions with monosynaptic connections with the amygdala, in autism from early to middle childhood. A total of 950 longitudinal structural MRI scans were acquired from 282 children (93 female) with autism and 128 children with typical development (61 female) at up to four time points (mean ages: 39, 52, 64, and 137 months, respectively). Volumes from 32 amygdala-connected brain regions were examined using mixed effects multivariate distance matrix regression. The Social Responsiveness Scale-2 was administered to assess degree of autistic traits and social impairments. The amygdala-connected network exhibited persistent diagnostic differences (p values ≤ 0.03) that increased over time (p values ≤ 0.02). These differences were most prominent in autistics with more impacted social functioning at baseline. This pattern was not observed across regions without monosynaptic amygdala connection. We observed qualitative sex differences. In males, the bilateral subgenual anterior cingulate cortices were most affected, while in females the left fusiform and superior temporal gyri were most affected. In conclusion, (1) autism is associated with widespread alterations to the development of brain regions connected with the amygdala, which were associated with autistic social behaviors; and (2) autistic males and females exhibited different patterns of alterations, adding to a growing body of evidence of sex differences in the neurobiology of autism.SIGNIFICANCE STATEMENT Global patterns of development across brain regions with monosynaptic connection to the amygdala differentiate autism from typical development, and are modulated by social functioning in early childhood. Alterations to brain regions within the amygdala-connected network differed in males and females with autism. Results also indicate larger volumetric differences in regions having monosynaptic connection with the amygdala than in regions without monosynaptic connection.

Evaluation of the Potential Utility of an Artificial Intelligence Chatbot in Gastroesophageal Reflux Disease Management.

INTRODUCTION: Artificial intelligence chatbots could serve as an information resource for patients and a tool for clinicians. Their ability to respond appropriately to questions regarding gastroesophageal reflux disease is unknown. METHODS: Twenty-three prompts regarding gastroesophageal reflux disease management were submitted to ChatGPT, and responses were rated by 3 gastroenterologists and 8 patients. RESULTS: ChatGPT provided largely appropriate responses (91.3%), although with some inappropriateness (8.7%) and inconsistency. Most responses (78.3%) contained at least some specific guidance. Patients considered this a useful tool (100%). DISCUSSION: ChatGPT's performance demonstrates the potential for this technology in health care, although also its limitations in its current state.

NR4A1 modulates intestinal smooth muscle cell phenotype and dampens inflammation-associated intestinal remodeling.

Stricture formation is a common complication of Crohn's disease (CD), driven by enhanced deposition of extracellular matrix (ECM) and expansion of the intestinal smooth muscle layers. Nuclear receptor subfamily 4 group A member 1 (NR4A1) is an orphan nuclear receptor that exhibits anti-proliferative effects in smooth muscle cells (SMCs). We hypothesized that NR4A1 regulates intestinal SMC proliferation and muscle thickening in the context of inflammation. Intestinal SMCs isolated from Nr4a1+/+ and Nr4a1-/- littermates were subjected to shotgun proteomic analysis, proliferation, and bioenergetic assays. Proliferation was assessed in the presence and absence of NR4A1 agonists, cytosporone-B (Csn-B) and 6-mercaptopurine (6-MP). In vivo, we compared colonic smooth muscle thickening in Nr4a1+/+ and Nr4a1-/- mice using the chronic dextran sulfate sodium (DSS) model of colitis. Second, SAMP1/YitFc mice (a model of spontaneous ileitis) were treated with Csn-B and small intestinal smooth muscle thickening was assessed. SMCs isolated from Nr4a1-/- mice exhibited increased abundance of proteins related to cell proliferation, metabolism, and ECM production, whereas Nr4a1+/+ SMCs highly expressed proteins related to the regulation of the actin cytoskeleton and contractile processes. SMCs isolated from Nr4a1-/- mice exhibited increased proliferation and alterations in cellular metabolism, whereas activation of NR4A1 attenuated proliferation. In vivo, Nr4a1-/- mice exhibited increased colonic smooth muscle thickness following repeated cycles of DSS. Activating NR4A1 with Csn-B, in the context of established inflammation, reduced ileal smooth muscle thickening in SAMP1/YitFc mice. Targeting NR4A1 may provide a novel approach to regulate intestinal SMC phenotype, limiting excessive proliferation that contributes to stricture development in CD.

The real unmet need: A multifactorial approach for identifying sensitized kidney candidates with low access to transplant.

BACKGROUND: At the start of 2020, the kidney waiting list consisted of 2526 candidates with a calculated panel reactive antibody (CPRA) of 99.9% or greater, a cohort demonstrated in published research to have meaningfully lower than average access to transplantation even under the revised kidney allocation system (KAS). METHODS: This was a retrospective analysis of US kidney registrations using data from the OPTN [Reference (https://optn.transplant.hrsa.gov/data/about-data/)]. The period-prevalent study cohort consisted of US kidney-alone registrations who waited at least 1 day between April 1, 2016, when HLA DQ-Alpha and DP-Beta unacceptable antigen data became available in OPTN data collection, to December 31, 2019. Poisson rate regression was used to model deceased donor kidney transplant rates per active year waiting and using an offset term to account for differential at-risk periods. Median time to transplant was estimated for each IRR group using the Kaplan-Meier method. Sensitivity analyses were included to address geographic variation in supply-to-demand ratios and differences in dialysis time or waiting time. RESULTS: In this study, we found 1597 additional sensitized (CPRA 50-<99.9%) candidates with meaningfully lower than average access to transplant when simultaneously taking into account CPRA and other factors. In combination with CPRA, candidate blood type, Estimated Post-Transplant Survival Score (EPTS), and presence of other antibody specificities beyond those in the current, 5-locus CPRA were found to influence the likelihood of transplant. CONCLUSION: In total, this suggests approximately 4100 sensitized candidates are on the waiting list who represent a community of disadvantaged patients who may benefit from progressive therapies and interventions to facilitate incompatible transplantation. Though associated with higher risks, such interventions may nevertheless be more attractive than remaining on dialysis with the associated accumulation of mortality risk over time.

The Murine MHC Class II Super Enhancer IA/IE-SE Contains a Functionally Redundant CTCF-Binding Component and a Novel Element Critical for Maximal Expression.

In both humans and mice, CTCF-binding elements form a series of interacting loops across the MHC class II (MHC-II) locus, and CTCF is required for maximal MHC-II gene expression. In humans, a CTCF-bound chromatin insulator termed XL9 and a super enhancer (SE) DR/DQ-SE situated in the intergenic region between HLA-DRB1 and HLA-DQA1 play critical roles in regulating MHC-II expression. In this study, we identify a similar SE, termed IA/IE-SE, located between H2-Eb1 and H2-Aa of the mouse that contains a CTCF site (C15) and a novel region of high histone H3K27 acetylation. A genetic knockout of C15 was created and its role on MHC-II expression tested on immune cells. We found that C15 deletion did not alter MHC-II expression in B cells, macrophages, and macrophages treated with IFN-γ because of functional redundancy of the remaining MHC-II CTCF sites. Surprisingly, embryonic fibroblasts derived from C15-deleted mice failed to induce MHC-II gene expression in response to IFN-γ, suggesting that at least in this developmental lineage, C15 was required. Examination of the three-dimensional interactions with C15 and the H2-Eb1 and H2-Aa promoters identified interactions within the novel region of high histone acetylation within the IA/IE-SE (termed N1) that contains a PU.1 binding site. CRISPR/Cas9 deletion of N1 altered chromatin interactions across the locus and resulted in reduced MHC-II expression. Together, these data demonstrate the functional redundancy of the MHC-II CTCF elements and identify a functionally conserved SE that is critical for maximal expression of MHC-II genes.

Trajectories of depression among patients in treatment for opioid use disorder: A growth mixture model secondary analysis of the XBOT trial.

BACKGROUND AND OBJECTIVES: To inform clinical practice, we identified subgroups of adults based on levels of depression symptomatology over time during opioid use disorder (OUD) treatment. METHODS: Participants were 474 adults in a 24-week treatment trial for OUD. Depression symptoms were measured using the 17-item Hamilton Depression Rating Scale (HAM-D) at nine-time points. This was a secondary analysis of the Clinical Trials Network Extended-Release Naltrexone versus Buprenorphine for Opioid Treatment (XBOT) trial using a growth mixture model. RESULTS: Three distinct depression trajectories were identified: Class 1 High Recurring-10% with high HAM-D with initial partial reductions (of HAM-D across time), Class 2 Persistently High-5% with persistently high HAM-D, and Class 3 Low Declining-85% of the participants, with low HAM-D with early sustained reductions. The majority (low declining) had levels of depression that improved in the first 4 weeks and then stabilized across the treatment period. In contrast, 15% (high recurring and persistently high) had high initial levels that were more variable across time. The persistently high class had higher rates of opioid relapse. DISCUSSION AND CONCLUSIONS: In this OUD sample, most depressive symptomatology was mild and improved after medication treatment for opioid use disorder (MOUD). Smaller subgroups had higher depressive symptoms that persisted or recurred after the initiation of MOUD. Depressive symptoms should be followed in patients initiating treatment for OUD, and when persistent, should prompt further evaluation and consideration of antidepressant treatment. SCIENTIFIC SIGNIFICANCE: This study is the first to identify three distinct depression trajectories among a large clinical sample of individuals in MOUD treatment.

A graph-based approach for the visualisation and analysis of bacterial pangenomes.

BACKGROUND: The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. RESULTS: Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences. CONCLUSIONS: We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.

Sex-dependent structure of socioemotional salience, executive control, and default mode networks in preschool-aged children with autism.

The structure of large-scale intrinsic connectivity networks is atypical in adolescents diagnosed with autism spectrum disorder (ASD or autism). However, the degree to which alterations occur in younger children, and whether these differences vary by sex, is unknown. We utilized structural magnetic resonance imaging (MRI) data from a sex- and age- matched sample of 122 autistic and 122 typically developing (TD) children (2-4 years old) to investigate differences in underlying network structure in preschool-aged autistic children within three large scale intrinsic connectivity networks implicated in ASD: the Socioemotional Salience, Executive Control, and Default Mode Networks. Utilizing structural covariance MRI (scMRI), we report network-level differences in autistic versus TD children, and further report preliminary findings of sex-dependent differences within network topology.

Design of Volumetric Nanolayers via Rapid Proteolysis of Silk Fibroin for Tissue Engineering.

Various methods have been studied to make a regenerated silk fibroin solution. However, most of them take too much time and effort to liquefy. Here, we report that a regenerated silk fibroin solution could be prepared within seconds through acid proteolysis for the first time. The solubilized fibroin could be applied to advanced tissue engineering. Our method shortened the production time to one day (more than 10 times) compared to the general fibroin solution preparation method. It was confirmed that the initial protein affinity nearly doubled from 0.028 to 0.076 µg·mm-2 in FF(ac) compared to FF(aq). A fibroin nanofiber layer having a volumetric hierarchical structure was prepared by electrospinning an acid-proteolyzed fibroin solution, followed by gas foaming. In vitro results of cell adhesion and proliferation capacity of the gas-foamed scaffold were not significantly different compared to the two-dimensional (2D) fibroin nanofiber membrane, overcoming the limitations of volumetric nanofiber scaffolds. We are confident that our research will greatly contribute to the development of regenerative engineering using other proteins.