Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin.

Advances in the study of neurological conditions have been possible because of pluripotent stem cell technologies and organoids. Studies have described the generation of neural ectoderm-derived retinal and brain structures from pluripotent stem cells. However, the field is still troubled by technical challenges, including high culture costs and variability. Here, we describe a simple and economical protocol that reproducibly gives rise to the neural retina and cortical brain regions from confluent cultures of stem cells. The spontaneously generated cortical organoids are transcriptionally comparable with organoids generated by other methods. Furthermore, these organoids showed spontaneous functional network activity and proteomic analysis confirmed organoids maturity. The generation of retinal and brain organoids in close proximity enabled their mutual isolation. Suspension culture of this complex organoid system demonstrated the formation of nerve-like structures connecting retinal and brain organoids, which might facilitate the investigation of neurological diseases of the eye and brain.

Navigating Pandemic Moral Distress at Home and at Work: Frontline Workers' Experiences.

Background: During the COVID-19 pandemic, frontline workers faced a series of challenges balancing family and work responsibilities. These challenges included making decisions about how to reduce COVID-19 exposure to their families while still carrying out their employment duties and caring for their children. We sought to understand how frontline workers made these decisions and how these decisions impacted their experiences.Methods: Between October 2020 and May 2021, we conducted 61 semi-structured interviews in English or Spanish, with individuals who continued to work outside of the home during the pandemic and had children living at home. Interviews were recorded, transcribed verbatim, and analyzed using abductive methods.Results: Frontline workers experienced moral distress, the inability to act in accordance with their values and obligations because of internal or external constraints. Their moral distress was a result of the tensions they felt as workers and parents, which sometimes led them to feel like they had to compromise on either or both responsibilities. Individuals felt morally conflicted because 1) their COVID-19 work exposures presented risk that often jeopardized their family's health; 2) their work hours often conflicted with their increased childcare responsibilities; and 3) they felt a duty to their colleagues, patients/customers, and communities to continue to show-up to work.Conclusions: Our findings point to a need to expand the concept of moral distress to include the perspectives of frontline workers outside of the healthcare professions and the fraught decisions that workers make outside of work that may impact their moral distress. Expanding the concept of moral distress also allows for a justice-based framing that can focus attention on the disparities inherent in much frontline work and can justify programmatic recommendations, like increasing paid childcare opportunities, to alleviate moral distress.

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity.

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.

Decontaminating N95 respirators during the COVID-19 pandemic: simple and practical approaches to increase decontamination capacity, speed, safety and ease of use.

BACKGROUND: The COVID-19 pandemic has caused a severe shortage of personal protective equipment (PPE), especially N95 respirators. Efficient, effective and economically feasible methods for large-scale PPE decontamination are urgently needed. AIMS: (1) to develop protocols for effectively decontaminating PPE using vaporized hydrogen peroxide (VHP); (2) to develop novel approaches that decrease set-up and take-down time while also increasing decontamination capacity; (3) to test decontamination efficiency for N95 respirators heavily contaminated by make-up or moisturizers. METHODS: We converted a decommissioned Biosafety Level 3 laboratory into a facility that could be used to decontaminate N95 respirators. N95 respirators were hung on metal racks, stacked in piles, placed in paper bags or covered with make-up or moisturizer. A VHP® VICTORY™ unit from STERIS was used to inject VHP into the facility. Biological and chemical indicators were used to validate the decontamination process. FINDINGS: N95 respirators individually hung on metal racks were successfully decontaminated using VHP. N95 respirators were also successfully decontaminated when placed in closed paper bags or if stacked in piles of up to six. Stacking reduced the time needed to arrange N95 respirators for decontamination by approximately two-thirds while almost tripling facility capacity. Make-up and moisturizer creams did not interfere with the decontamination process. CONCLUSIONS: Respirator stacking can reduce the hands-on time and increase decontamination capacity. When personalization is needed, respirators can be decontaminated in labelled paper bags. Make up or moisturizers do not appear to interfere with VHP decontamination.

Functional MRI for language lateralization in individuals with intellectual and cognitive dysfunction: Two clinical case examples.

OBJECTIVE: Task-based functional MRI (fMRI) is a common non-invasive method of confirming hemispheric language dominance prior to neurosurgery in epilepsy. However, the use of this method is not recommended for individuals with cognitive dysfunction and in those with IQ below 70 due to concerns about accuracy of task performance in the scanner. This manuscript describes successful use of task-based functional MRI to lateralize language dominance in two individuals with cognitive dysfunction and intellectual disability. METHODS: Two patients completed a pre-surgical epilepsy work-up at the QEII Health Sciences Centre in Halifax, Nova Scotia, which included comprehensive neuropsychological assessment. They also completed an fMRI paradigm that involved semantic category fluency, sentence completion, naming to description and passage listening tasks with stimuli delivered both visually and auditorily. RESULTS: In both cases, fMRI maps were successful in lateralizing language dominance in relation to other clinical data, including intraoperative cortical mapping in one of the cases. CONCLUSIONS: This manuscript is the first to demonstrate that task-based fMRI can be used successfully to lateralize language in adult patients with cognitive and intellectual disabilities, and is the first to propose a specific paradigm for this purpose.

"It's Just Another Added Benefit": Women's Experiences with Employment-Based Egg Freezing Programs.

BACKGROUND: In 2014, companies began covering the costs of egg freezing for their employees. The adoption of this benefit was highly contentious. Some argued that it offered women more reproductive autonomy, buying time to succeed in their careers and postpone childbearing. Others suggested this benefit might place inappropriate pressure on women, unduly influencing them to freeze their eggs to prioritize their career over reproduction. Although ethical problems with this benefit have been explored, there has not been research analyzing the perspectives of women working for companies that offer employer-based egg freezing. Furthermore, existing empirical studies often focus on the experiences of egg freezers rather than the young women thinking about, but not yet using, this technology. Methods: Through in-depth semi-structured interviews, we explore the perceptions and attitudes of 25 women employees of companies with employer-based egg freezing. Results: These women describe delaying childbearing for a multitude of reasons, including not having a partner, and the desire to achieve social and career goals. Many women did not know that their employers covered egg freezing before the interview (44%; 11/24), suggesting this benefit is not essential to their career and family-building decisions. While women did not describe pressure to use this technology, they did describe how this benefit would not solve the difficulties of becoming a mother while excelling in their careers. Conclusion: Although women may not feel pressure to freeze their eggs and delay childbearing, they still feel constricted in their reproductive options. While employer programs may offer women the ability to delay childbearing, many saw this delay as postponing problems with work-life balance rather than solving them. We suggest that sociocultural shifts, such as workplace daycare, flexible workplace hours, and acceptability of non-biological parenthood, might allow women to feel more empowered about their reproduction choices.

Use, re-use or discard? Quantitatively defined variance in the functional integrity of N95 respirators following vaporized hydrogen peroxide decontamination during the COVID-19 pandemic.

BACKGROUND: Coronavirus disease 2019 has stretched the ability of many institutions to supply needed personal protective equipment, especially N95 respirators. N95 decontamination and re-use programmes provide one potential solution to this problem. Unfortunately, a comprehensive evaluation of the effects of decontamination on the fit of various N95 models using a quantitative fit test (QNFT) approach is lacking. AIMS: To investigate the effects of up to eight rounds of vaporized hydrogen peroxide (VHP) decontamination on the fit of N95 respirators currently in use in a hospital setting, and to examine if N95 respirators worn by one user can adapt to the face shape of a second user with no compromise to fit following VHP decontamination. METHODS: The PortaCount Pro+ Respirator Fit Tester Model 8038 was used to quantitatively define functional integrity, measured by fit, of N95 respirators following decontamination with VHP. FINDINGS: There was an observable downward trend in the functional integrity of Halyard Fluidshield 46727 N95 respirators throughout eight cycles of decontamination with VHP. Functional integrity of 3M 1870 N95 respirators was reduced significantly after the respirator was worn, decontaminated with VHP, and then quantitatively fit tested on a second user. Furthermore, inconsistencies between qualitative fit test and QNFT results were uncovered that may have strong implications on the fit testing method used by institutions. CONCLUSIONS: The data revealed variability in the functional integrity of different N95 models after VHP decontamination, and exposed potential limitations of N95 decontamination and re-use programmes.

The role of PAs in providing mental health care.

The prevalence of psychiatric and substance use disorders in the United States is rising and of growing concern. Because such behavioral conditions are widespread, one approach is to collaborate with various medical professionals to help offset this demand. To address this issue, the frequency and types of mental health conditions encountered by physician assistants (PAs) were assessed. The National Commission on the Certification of Physician Assistants Practice Analysis was examined for the types of mental health conditions encountered across the spectrum of medical and surgical practices. The findings reveal that, in 2015, at least 62% of PAs saw and evaluated mental health conditions and behavioral disorders at least weekly in their settings. These patient diagnoses were seen with variability based on the specialty of the PA. The highest percentage of cases reported by PAs were in psychiatry, followed by general internal medicine, emergency medicine, family medicine, and hospital medicine. With the profession projected to grow, recruiting, retaining, and integrating more PAs into mental health care is a suggested strategy for addressing national provider shortages.

An Update on Health-Related Quality of Life and Patient-Reported Outcomes in Hidradenitis Suppurativa.

Hidradenitis suppurativa is a common inflammatory skin condition which causes recurrent abscesses, sinuses and scarring in the axillae, groin and inframammary areas. As well as causing significant physical distress due to pain and discharge, the condition impacts psychological well-being with markedly impaired quality of life. Patients suffer pain, embarrassment and psychological distress with impairment of their work and intimate relationships marking it as one of the most distressing dermatological conditions. Numerous studies have documented markers of psychological distress encompassing the physical effects such as pain and itch, affects on mood and impaired function.

Epigenetic reprogramming at estrogen-receptor binding sites alters 3D chromatin landscape in endocrine-resistant breast cancer.

Endocrine therapy resistance frequently develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine-resistant breast cancer cells and that the differential interactions are enriched for resistance-associated genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites, and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. We observe that loss of 3D chromatin interactions often occurs coincidently with hypermethylation and loss of ER binding. Alterations in active A and inactive B chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer.

Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains.

The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood. Here we perform RNAi knockdown to reduce CTCF levels and reveal a shared subset of CTCF-bound sites are robustly resistant to protein depletion. The 'persistent' CTCF sites are enriched at domain boundaries and chromatin loops constitutive to all cell types. CRISPR-Cas9 deletion of 2 persistent CTCF sites at the boundary between a long-range epigenetically active (LREA) and silenced (LRES) region, within the Kallikrein (KLK) locus, results in concordant activation of all 8 KLK genes within the LRES region. CTCF genome-wide depletion results in alteration in Topologically Associating Domain (TAD) structure, including the merging of TADs, whereas TAD boundaries are not altered where persistent sites are maintained. We propose that the subset of essential CTCF sites are involved in cell-type constitutive, higher order chromatin architecture.

A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation.

Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active regulatory regions associated with gene expression. Although the Tip60 complex is proposed to acetylate H2A.Z, functional studies suggest additional enzymes are involved. Here, we show that p300 acetylates H2A.Z at multiple lysines. In contrast, we found that although Tip60 does not efficiently acetylate H2A.Z in vitro, genetic inhibition of Tip60 reduces H2A.Zac in cells. Importantly, we found that interaction between the p300-bromodomain and H4 acetylation (H4ac) enhances p300-driven H2A.Zac. Indeed, H2A.Zac and H4ac show high genomic overlap, especially at active promoters. We also reveal unique chromatin features and transcriptional states at enhancers correlating with co-occurrence or exclusivity of H4ac and H2A.Zac. We propose that differential H4 and H2A.Z acetylation signatures can also define the enhancer state. In conclusion, we show both Tip60 and p300 contribute to H2A.Zac and reveal molecular mechanisms of writer/reader crosstalk between H2A.Z and H4 acetylation through p300.

PSEN1ΔE9, APPswe, and APOE4 Confer Disparate Phenotypes in Human iPSC-Derived Microglia.

Here we elucidate the effect of Alzheimer disease (AD)-predisposing genetic backgrounds, APOE4, PSEN1ΔE9, and APPswe, on functionality of human microglia-like cells (iMGLs). We present a physiologically relevant high-yield protocol for producing iMGLs from induced pluripotent stem cells. Differentiation is directed with small molecules through primitive erythromyeloid progenitors to re-create microglial ontogeny from yolk sac. The iMGLs express microglial signature genes and respond to ADP with intracellular Ca2+ release distinguishing them from macrophages. Using 16 iPSC lines from healthy donors, AD patients and isogenic controls, we reveal that the APOE4 genotype has a profound impact on several aspects of microglial functionality, whereas PSEN1ΔE9 and APPswe mutations trigger minor alterations. The APOE4 genotype impairs phagocytosis, migration, and metabolic activity of iMGLs but exacerbates their cytokine secretion. This indicates that APOE4 iMGLs are fundamentally unable to mount normal microglial functionality in AD.

DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns.

Promoter CpG islands are typically unmethylated in normal cells, but in cancer a proportion are subject to hypermethylation. Using methylome sequencing we identified CpG islands that display partial methylation encroachment across the 5' or 3' CpG island borders. CpG island methylation encroachment is widespread in prostate and breast cancer and commonly associates with gene suppression. We show that the pattern of H3K4me1 at CpG island borders in normal cells predicts the different modes of cancer CpG island hypermethylation. Notably, genetic manipulation of Kmt2d results in concordant alterations in H3K4me1 levels and CpG island border DNA methylation encroachment. Our findings suggest a role for H3K4me1 in the demarcation of CpG island methylation borders in normal cells, which become eroded in cancer.

PA practice analysis: Multidisciplinary tasks, knowledge, and skills.

In conducting its practice analysis, the National Commission on Certification of Physician Assistants incorporated new approaches in 2015. Twelve groups of PAs identified knowledge, tasks, and skills required for practice not only in primary care, but also in 11 practice focus areas (specialties). In addition, a list of diseases and disorders likely to be encountered was identified for each specialty. A representative sample of 15,771 certified PAs completed an online algorithm-driven survey and data were analyzed to determine how practice is the same for all PAs and how it differs depending on the practice focus. Larger differences between PAs in different specialties were seen in the frequency ratings of diseases and disorders encountered than for ratings of task, knowledge, and skill statements. Distinctions between PAs in primary care and those in other specialties were more pronounced, as the specialty was more divergent from primary care.

Living Outside the Gender Box in Mexico: Testimony of Transgender Mexican Asylum Seekers.

OBJECTIVES: To explore preimmigration experiences of violence and postimmigration health status in male-to-female transgender individuals (n = 45) from Mexico applying for asylum in the United States. METHODS: We used a document review process to examine asylum declarations and psychological evaluations of transgender Mexican asylum seekers in the United States from 2012. We coded documents in 2013 and 2014 using NVivo, a multidisciplinary team reviewed them, and then we analyzed them for themes. RESULTS: Mexican transgender asylum applicants experienced pervasive verbal, physical, and sexual abuse from multiple sources, including family, school, community, and police. Applicants also experienced discrimination in school and in the workplace. Applicants immigrated to the United States to escape persistent assaults and threats to their life. Applicants suffered health and psychological effects from their experiences in Mexico that affected opportunities in the United States for employment, education, and social inclusion. CONCLUSIONS: Additional social protections for transgender individuals and antidiscrimination measures in Mexican schools and workplaces are warranted as are increased mental health assessment and treatment, job training, and education services for asylum seekers in the United States.

Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning.

Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy, we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. This opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.

Data systems for the Linac coherent light source.

The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available.

Prolonged constant load cycling exercise is associated with reduced gross efficiency and increased muscle oxygen uptake.

This study investigated the effects of prolonged constant load cycling exercise on cycling efficiency and local muscle oxygen uptake responses. Fourteen well-trained cyclists each completed a 2-h steady-state cycling bout at 60% of their maximal minute power output to assess changes in gross cycling efficiency (GE) and muscle oxygen uptake (mVO2 ) at time points 5, 30, 60, 90, and 120 min. Near-infrared spatially resolved spectroscopy (NIRS) was used to continually monitor tissue oxygenation of the Vastus Lateralis muscle, with arterial occlusions (OCC) applied to assess mVO2 . The half-recovery time of oxygenated hemoglobin (HbO2 ) was also assessed pre and post the 2-h cycling exercise by measuring the hyperemic response following a 5-min OCC. GE significantly declined during the 2-h cycling bout (18.4 ± 1.6 to 17.4 ± 1.4%; P < 0.01). Conversely, mVO2 increased, being significantly higher after 90 and 120 min than at min 5 (+0.04 mlO2 /min/100 g; P = 0.03). The half-recovery time for HbO2 was increased comparing pre and post the 2-h cycling exercise (+7.1 ± 19s), albeit not significantly (d: 0.48; P = 0.27). This study demonstrates that GE decreases during prolonged constant load cycling exercise and provides evidence of an increased mVO2 , suggestive of progressive mitochondrial or contractile inefficiency.