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Genome-wide association studies have identified risk loci linked to inflammatory bowel disease (IBD)(1)—a complex chronic inflammatory disorder of the gastrointestinal tract. The increasing prevalence of IBD in industrialized countries and the augmented disease risk observed in migrants who move into areas of higher disease prevalence suggest that environmental factors are also important determinants of IBD susceptibility and severity(2). However, the identification of environmental factors relevant to IBD and the mechanisms by which they influence disease has been hampered by the lack of platforms for their systematic investigation. Here we describe an integrated systems approach, combining publicly available databases, zebrafish chemical screens, machine learning and mouse preclinical models to identify environmental factors that control intestinal inflammation. This approach established that the herbicide propyzamide increases inflammation in the small and large intestine. Moreover, we show that an AHR–NF-κB–C/EBPβ signalling axis operates in T cells and dendritic cells to promote intestinal inflammation, and is targeted by propyzamide. In conclusion, we developed a pipeline for the identification of environmental factors and mechanisms of pathogenesis in IBD and, potentially, other inflammatory diseases.

BackgroundA rare and fatal disease resembling mucopolysaccharidosis in infants, is caused by impaired intracellular endocytic trafficking due to deficiency of core components of the intracellular membrane-tethering protein complexes, HOPS and CORVET.MethodsWhole Exome Sequencing identified a novel VPS33A mutation in a patient suffering from a variant form of mucopolysaccharidosis. Electron and confocal microscopy, immunoblotting, and glycosphingolipid trafficking experiments were undertaken to investigate the effects of the mutant VPS33A in patient-derived skin fibroblasts.ResultsWe describe an attenuated juvenile form of VPS33A-related syndrome - mucopolysaccharidosis plus in a man who is homozygous for a hitherto unknown missense mutation (NM_022916.4: c.599 G>C; R200P) in a conserved region of the VPS33A gene. Urinary glycosaminoglycan analysis revealed increased heparan, dermatan sulphates and hyaluronic acid. We showed decreased abundance of VPS33A in patient derived fibroblasts and provided evidence that the R200P mutation leads to destabilisation of the protein and proteasomal degradation. As in the infantile form of mucopolysaccharidosis plus, the endocytic compartment in the fibroblasts also expanded – a phenomenon accompanied by increased endolysosomal acidification and impaired intracellular glycosphingolipid trafficking. Experimental treatment of the patient’s cultured fibroblasts with the proteasome inhibitor, bortezomib, or exposure to an inhibitor of glucosylceramide synthesis, eliglustat, improved glycosphingolipid trafficking.ConclusionTo our knowledge this is the first report of an attenuated juvenile form of VPS33A insufficiency characterised by appreciable residual endosomal-lysosomal trafficking and a milder mucopolysaccharidosis plus than the disease in infants. Our findings expand the proof of concept of redeploying clinically approved drugs for therapeutic exploitation in patients with juvenile as well as infantile forms of mucopolysaccharidosis plus disease.

The redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) is important for the binding of SARS-2-S to angiotensin-converting enzyme 2 (ACE2), suggesting that drugs with a functional thiol group (“thiol drugs”) may cleave cystines to disrupt SARS-CoV-2 cell entry. In addition, neutrophil-induced oxidative stress is a mechanism of COVID-19 lung injury, and the antioxidant and anti-inflammatory properties of thiol drugs, especially cysteamine, may limit this injury. To first explore the antiviral effects of thiol drugs in COVID-19, we used an ACE-2 binding assay and cell entry assays utilizing reporter pseudoviruses and authentic SARS-CoV-2 viruses. We found that multiple thiol drugs inhibit SARS-2-S binding to ACE2 and virus infection. The most potent drugs were effective in the low millimolar range, and IC50 values followed the order of their cystine cleavage rates and lower thiol p Ka values. To determine if thiol drugs have antiviral effects in vivo and to explore any anti-inflammatory effects of thiol drugs in COVID-19, we tested the effects of cysteamine delivered intraperitoneally to hamsters infected with SARS-CoV-2. Cysteamine did not decrease lung viral infection, but it significantly decreased lung neutrophilic inflammation and alveolar hemorrhage. We speculate that the concentration of cysteamine achieved in the lungs with intraperitoneal delivery was insufficient for antiviral effects but sufficient for anti-inflammatory effects. We conclude that thiol drugs decrease SARS-CoV-2 lung inflammation and injury, and we provide rationale for future studies to test if direct (aerosol) delivery of thiol drugs to the airways might also result in antiviral effects.

We describe 33 cases of myxoid pseudotumor involving the renal sinus from 31 patients. Patients included 21 men and 10 women, ages 30 to 95 years. Twenty-seven cases (82%) had an associated malignancy, including urothelial carcinoma of the renal pelvis (22 cases), clear cell renal cell carcinoma (3 cases), urothelial carcinoma of the bladder (1 case), and poorly differentiated carcinoma of uncertain lineage (1 case). The remaining 6 (18%) had no associated malignancy and included 3 nephrectomies for ureteral stricture, 2 ureteropelvic junction repairs, and 1 resection of a "periureteral mass" (subsequently shown to be myxoid pseudotumor). Myxoid pseudotumor was identified by preoperative computed tomography imaging in 2 patients (6%) and identified by the gross dissector in 9 cases (27%). The mean size was 14 mm (range: 5 to 38 mm). All cases had an admixture of adipocytes, myxoid stromal matrix, variable collagenization, and a hypocellular population of bland spindled and stellate stromal cells. No multilobated atypical stromal cells were present. Clinical follow-up was available for 28 patients (90%), ranging from 1 to 132 months (mean: 24.6 mo). No patients had adverse events related to the myxoid pseudotumor. Myxoid pseudotumor of the renal sinus is often associated with a variety of adjacent neoplastic and non-neoplastic conditions and may present as a mass lesion detectable by imaging and/or gross inspection. Awareness of this benign process is important to avoid confusion with a neoplasm, especially liposarcoma.

Scholars have found that nonviolent resistance is more effective than violence at promoting post-campaign democratization. We explore whether this relationship extends to judicial systems, specifically. Courts have been shown to be important for promoting and protecting economic development and political rights, yet they have been largely ignored in quantitative studies of post-conflict democratization. We posit that leaders who hold power after domestic unrest will be more inclined to use independent courts as a mechanism to prevent future campaigns–but they do so primarily when fearing a significant mobilization threat and when expecting legal action to be an acceptable channel for dispute resolution by dissidents. As such, we anticipate that levels of judicial independence are higher following nonviolent campaigns as compared to violent conflicts. Using quantitative data from violent and nonviolent campaigns globally, we find that judicial independence is indeed higher in the aftermath of nonviolent, as compared to violent, resistance campaigns. Furthermore, a campaign’s outcome does not matter; post-conflict judicial independence appears to be associated with tactics, not dissident success.

Bariatric surgery improves glucose homeostasis but the underlying mechanisms are not fully elucidated. Here, we show that the expression of sodium glucose cotransporter-2 (SGLT2/Slc5a2) is reduced in the kidney of lean and obese mice following vertical sleeve gastrectomy (VSG). Indicating an important contribution of altered cotransporter expression to the impact of surgery, inactivation of the SGLT2/Slc5a2 gene by CRISPR/Cas9 attenuated the effects of VSG, with glucose excursions following intraperitoneal injection lowered by ~30% in wild-type mice but by ~20% in SGLT2 null animals. The effects of the SGLT2 inhibitor dapaglifozin were similarly blunted by surgery. Unexpectedly, effects of dapaglifozin were still observed in SGLT2 null mice, consistent with the existence of metabolically beneficial off-target effects of SGLT2 inhibitors. Thus, we describe a new mechanism involved in mediating the glucose lowering effects of bariatric surgery.

The assemblage of fungi including unicellular yeasts in schools is understudied. We conducted an environmental study to characterize fungal communities in classroom floor dust. We collected 500 samples from 50 elementary schools in Philadelphia, PA, and evaluated room dampness/mold conditions. Genomic DNA from dust was extracted for internal transcribed spacer 1 Illumina MiSeq sequencing to identify operational taxonomic units (OTUs) organized from DNA sequences. Differential abundance analyses were performed to examine significant differences in abundance among groups. We identified 724 genera from 1490 OTUs. The genus

The potential for work to be a risk factor for coronavirus disease 2019 (COVID-19) was recognized early in the pandemic based on the likelihood of work-related differences in exposures to COVID-19 in different occupations. Due to intense demands of the pandemic, implementation of recommendations to collect information on occupation in relation to COVID-19 has been uneven across the United States. The objective of this study was to investigate COVID-19 test positivity by occupation.We analyzed data collected from September 8 to November 30, 2020, by the Delphi Group at Carnegie Mellon University US COVID-19 Trends and Impact Survey, offered daily to a random sample of US-based Facebook users aged 18 years or older, who were invited via a banner in their news feed. Our focus was ever testing positive for COVID-19 in respondents working outside the home for pay in the past 4 weeks.The major occupational groups of "Production", "Building and grounds cleaning and maintenance," "Construction and extraction," "Healthcare support," and "Food preparation and serving" had the five highest test positivity percentages (16.7%-14.4%). Highest detailed occupational categories (28.6%-19.1%) were "Massage therapist," "Food processing worker," "Bailiff, correctional officer, or jailer," "Funeral service worker," "First-line supervisor of production and operating workers," and "Nursing assistant or psychiatric aide." Differences in test positivity by occupation remained after adjustment for age, gender, and pre-existing medical conditions.Information on differences in test positivity by occupation can aid targeting of messaging for vaccination and testing and mitigation strategies for the current and future respiratory infection epidemics and pandemics. These results, obtained before availability of COVID-19 vaccines, can form a basis for comparison to evaluate impacts of vaccination and subsequent emergence of viral variants.

Palm-leaf manuscripts are an important part of the heritage of the Lanna culture of northern Thailand. The purpose of this article is to explore the practices and attitudes towards managing palm-leaf manuscripts in three communities in northern Thailand with a view to developing a community-centric understanding of sustainable care for palm-leaf manuscripts. The study was based on interviews, which were analysed thematically. It was found that Buddhist beliefs in earning merit and the cultural value of palm-leaf manuscripts underlie community involvement. Leadership was also important, although models of leadership were different in each case. External organizations such as universities play a key role in cataloguing, preserving and using palm-leaf manuscripts. Digitization, although central to the value to external organizations, does not really promote community access. Reflecting on the drivers and challenges in the three villages, a model of community-driven care for palm-leaf manuscripts is proposed.

This study analyzes the institutional variation across domestic legal systems, with a focus on common law system’s adherence to precedent and reduced recourse to judicial deference, as well as on the degree of independence afforded to courts. These institutional qualities of judiciaries provide the opportunity for courts to play a more active role in the implementation of post-conflict justice, increasing uncertainty for other policymakers concerning the ultimate contours of post-conflict justice processes. To reduce such uncertainty, policymakers ensconced in these types of institutional contexts will be less likely to implement post-conflict justice. Using data from the Post-Conflict Justice dataset, we find that states with common law systems are less likely to pursue and implement post-conflict justice compared to states with civil or Islamic law systems. Moreover, independent courts will be less likely to pursue mixed or restorative forms post-conflict justice, though the impact of judicial independence is weak overall.

Homologs of the mutagenic Escherichia coli DNA polymerase V (pol V) are encoded by numerous pathogens and mobile elements. We have used Rum pol (RumA′2B), from the integrative conjugative element (ICE), R391, as a model mobile element-encoded polymerase (MEPol). The highly mutagenic Rum pol is transferred horizontally into a variety of recipient cells, including many pathogens. Moving between species, it is unclear if Rum pol can function on its own or requires activation by host factors. Here, we show that Rum pol biochemical activity requires the formation of a physical mutasomal complex, Rum Mut, containing RumA′2B-RecA-ATP, with RecA being donated by each recipient bacteria. For R391, Rum Mut specific activities in vitro and mutagenesis rates in vivo depend on the phylogenetic distance of host-cell RecA from E. coli RecA. Rum pol is a highly conserved and effective mobile catalyst of rapid evolution, with the potential to generate a broad mutational landscape that could serve to ensure bacterial adaptation in antibiotic-rich environments leading to the establishment of antibiotic resistance.

Research-based Theater (RbT) combines research and theater to create novel opportunities for inquiry and knowledge translation. Ethical tensions are part of this process. We explore some tensions that can emerge through three types of ethics: professional ethics, institutional research ethics, and everyday ethics. We then propose a series of ethical guideposts developed by engaging RbT practitioners in reflecting on their practice. Like signs on a highway, ethical guideposts do not mandate a destination but rather flag that an approaching decision needs consideration. These guideposts seek to encourage greater attention to ethical aspects of RbT projects and to support ethical decision-making.

Dry eye disease is characterized by a persistently unstable or deficient tear film causing discomfort or visual impairment. Varenicline is a small-molecule nicotinic acetylcholine receptor agonist recently approved for use as a preservative-free nasal spray (OC-01 [varenicline solution] nasal spray [OC-01 VNS]) to treat signs and symptoms of dry eye disease, but its effect on conjunctival goblet cells has not been studied.In this phase 2, single-center, vehicle-controlled study, patients aged 18 years or more with a diagnosis of dry eye disease and Ocular Surface Disease IndexThe study randomized 18 patients (mean age 61 years); 6 received vehicle (3/6 [50%] female) and 12 patients received OC-01 VNS (11/12 [92%] female). OC-01 VNS treatment decreased mean goblet cell area (pre-treatment, 106.4 µmThis study demonstrated that a single administration of OC-01 0.06 mg VNS in patients with dry eye disease reduced conjunctival goblet cell area and perimeter, suggesting goblet cell degranulation and associated release of lubricating mucin. By activating the natural tear film, OC-01 VNS may provide benefits over topical medications.ClinicalTrials.gov, NCT03688802.

Bacterial spot of peach, caused by Xanthomonas arboricola pv. pruni, causes yield loss every year in southeastern U.S. peach orchards. Management is mainly driven by season-long applications of copper-based products, site location, and choice of cultivar. Although tolerance to copper has not been reported in X. arboricola pv. pruni in the United States, adaptation of populations from frequent use is a concern. We collected X. arboricola pv. pruni from shoot cankers, leaves, and fruit of cultivar O’Henry over 2 years from three conventional farms and one organic farm in South Carolina, one orchard per farm. The four farms had been using copper extensively for years to control bacterial spot. X. arboricola pv. pruni was isolated from four canker types (bud canker, tip canker, nonconcentric canker, and concentric canker) in early spring (bud break), as well as from leaf and fruit tissues later in the season at the phenological stages of pit hardening and final swell. X. arboricola pv. pruni was most frequently isolated from cankers of the organic farm (24% of the cankers) and most isolates (45%) came from bud cankers. X. arboricola pv. pruni isolates were assessed for sensitivity to copper using minimal glucose yeast agar and nutrient agar amended with 38 μg/ml or 51 μg/ml of Cu2+. Two phenotypes of copper tolerance in X. arboricola pv. pruni were discovered: low copper tolerance (LCT; growth up to 38 μg/ml Cu2+) and high copper tolerance (HCT; growth up to 51 μg/ml Cu2+). A total of 26 (23 LCT and 3 HCT) out of 165 isolates in 2018 and 32 (20 LCT and 12 HCT) out of 133 isolates in 2019 were tolerant to copper. Peach leaves on potted trees were sprayed with copper rates typically applied at the stages of delayed dormancy (high rate; 2,397 μg/ml Cu2+), shuck split (medium rate; 599 μg/ml Cu2+), and during summer cover sprays (low rate; 120 μg/ml Cu2+), and subsequently inoculated with sensitive, LCT, and HCT strains. Results indicated that the low and medium rates of copper reduced bacterial spot incidence caused by the sensitive strain but not by the LCT and HCT strains. This study confirms existence of X. arboricola pv. pruni tolerance to copper in commercial peach orchards in the southeastern United States, and suggests its contribution to bacterial spot development under current management practices.

When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic.

Single-stranded DNA gaps form within theE. colichromosome during replication, repair and recombination. However, information about the extent of ssDNA creation in the genome is limited. To complement a recent whole-genome sequencing study revealing ssDNA gap genomic distribution, size, and frequency, we used fluorescence microscopy to monitor the spatiotemporal dynamics of single-stranded DNA within liveE. colicells. The ssDNA was marked by a functional fluorescent protein fusion of the SSB protein that replaces the wild type SSB. During log-phase growth the SSB fusion produces a mixture of punctate foci and diffuse fluorescence spread throughout the cytosol. Many foci are clustered. Fluorescent markers of DNA polymerase III frequently co-localize with SSB foci, often localizing to the outer edge of the large SSB features. Novel SSB-enriched features form and resolve regularly during normal growth. UV irradiation induces a rapid increase in SSB foci intensity and produces large features composed of multiple partially overlapping foci. The results provide a critical baseline for further exploration of ssDNA generation during DNA metabolism. Alterations in the patterns seen in a mutant lacking RecB function tentatively suggest associations of particular SSB features with the repair of double strand breaks and post-replication gaps.

The bacterial RecF, RecO, and RecR proteins are an epistasis group involved in loading RecA protein into post-replication gaps. However, the targeting mechanism that brings these proteins to appropriate gaps is unclear. Here, we propose that targeting may involve a direct interaction between RecF and DnaN. In vivo, RecF is commonly found at the replication fork. Over-expression of RecF, but not RecO or a RecF ATPase mutant, is extremely toxic to cells. We provide evidence that the molecular basis of the toxicity lies in replisome destabilization. RecF over-expression leads to loss of genomic replisomes, increased recombination associated with post-replication gaps, increased plasmid loss, and SOS induction. Using three different methods, we document direct interactions of RecF with the DnaN β-clamp and DnaG primase that may underlie the replisome effects. In a single-molecule rolling-circle replication system in vitro, physiological levels of RecF protein trigger post-replication gap formation. We suggest that the RecF interactions, particularly with DnaN, reflect a functional link between post-replication gap creation and gap processing by RecA. RecF’s varied interactions may begin to explain how the RecFOR system is targeted to rare lesion-containing post-replication gaps, avoiding the potentially deleterious RecA loading onto thousands of other gaps created during replication.

In bacteria, the repair of post-replication gaps by homologous recombination requires the action of the recombination mediator proteins RecF, RecO and RecR. Whereas the role of the RecOR proteins to displace the single strand binding protein (SSB) and facilitate RecA loading is clear, how RecF mediates targeting of the system to appropriate sites remains enigmatic. The most prominent hypothesis relies on specific RecF binding to gap ends. To test this idea, we present a detailed examination of RecF and RecFR binding to more than 40 DNA substrates of varying length and structure. Neither RecF nor the RecFR complex exhibited specific DNA binding that can explain the targeting of RecF(R) to post-replication gaps. RecF(R) bound to dsDNA and ssDNA of sufficient length with similar facility. DNA binding was highly ATP-dependent. Most measured Kd values fell into a range of 60–180 nM. The addition of ssDNA extensions on duplex substrates to mimic gap ends or CPD lesions produces only subtle increases or decreases in RecF(R) affinity. Significant RecFR binding cooperativity was evident with many DNA substrates. The results indicate that RecF or RecFR targeting to post-replication gaps must rely on factors not yet identified, perhaps involving interactions with additional proteins.

Background National opioid-related overdose fatalities totaled 650,000 from 1999 to 2021. Some of the highest rates occurred in New Hampshire, where 40% of the population lives rurally. Medications for opioid use disorder (MOUD; methadone, buprenorphine, and naltrexone) have demonstrated effectiveness in reducing opioid overdose and mortality. Methadone access barriers disproportionally impact rural areas and naltrexone uptake has been limited. Buprenorphine availability has increased and relaxed regulations reduces barriers in general medical settings common in rural areas. Barriers to prescribing buprenorphine include lack of confidence, inadequate training, and lack of access to experts. To address these barriers, learning collaboratives have trained clinics on best-practice performance data collection to inform quality improvement (QI). This project sought to explore the feasibility of training clinics to collect performance data and initiate QI alongside clinics’ participation in a Project ECHO virtual collaborative for buprenorphine providers. Methods Eighteen New Hampshire clinics participating in a Project ECHO were offered a supplemental project exploring the feasibility of performance data collection to inform QI targeting increased alignment with best practice. Feasibility was assessed descriptively, through each clinic’s participation in training sessions, data collection, and QI initiatives. An end-of-project survey was conducted to understand clinic staff perceptions of how useful and acceptable they found the program. Results Five of the eighteen health care clinics that participated in the Project ECHO joined the training project, four of which served rural communities in New Hampshire. All five clinics met the criteria for engagement, as each clinic attended at least one training session, submitted at least one month of performance data, and completed at least one QI initiative. Survey results showed that while clinic staff perceived the training and data collection to be useful, there were several barriers to collecting the data, including lack of staff time, and difficulty standardizing documentation within the clinic electronic health record. Conclusions Results suggest that training clinics to monitor their performance and base QI initiatives on data has potential to impact clinical best practice. While data collection was inconsistent, clinics completed several data-informed QI initiatives, indicating that smaller scale data collection might be more attainable.

Neuropeptide Y (NPY) receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on Neuropeptide Y Receptors [158]) are activated by the endogenous peptides neuropeptide Y, neuropeptide Y-(3-36), peptide YY, PYY-(3-36) and pancreatic polypeptide (PP). The receptor originally identified as the Y3 receptor has been identified as the CXCR4 chemokine recepter (originally named LESTR, [139]). The y6 receptor is a functional gene product in mouse, absent in rat, but contains a frame-shift mutation in primates producing a truncated non-functional gene [84]. Three-dimensional structures have been determined for subtype active receptors Y1, Y2 and Y4 [211, 114] and inactive antagonist bound Y1 and Y2 receptors [240, 210]. Many of the agonists exhibit differing degrees of selectivity dependent on the species examined. For example, the potency of PP is greater at the rat Y4 receptor than at the human receptor [62]. In addition, many agonists lack selectivity for individual subtypes, but can exhibit comparable potency against pairs of NPY receptor subtypes, or have not been examined for activity at all subtypes. [125I]-PYY or [125I]-NPY can be used to label Y1, Y2, Y5 and y6 subtypes non-selectively, while [125I][cPP(1-7), NPY(19-23), Ala31, Aib32, Gln34]hPP may be used to label Y5 receptors preferentially (note that cPP denotes chicken peptide sequence and hPP is the human sequence).

Opioid and opioid-like receptors are activated by a variety of endogenous peptides including [Met]enkephalin (met), [Leu]enkephalin (leu), β-endorphin (β-end), α-neodynorphin, dynorphin A (dynA), dynorphin B (dynB), big dynorphin (Big dyn), nociceptin/orphanin FQ (N/OFQ); endomorphin-1 and endomorphin-2 are also potential endogenous peptides. The Greek letter nomenclature for the opioid receptors, μ, δ and κ, is well established, and NC-IUPHAR considers this nomenclature appropriate, along with the symbols spelled out (mu, delta, and kappa), and the acronyms, MOP, DOP, and KOP [124, 101, 92]. However the acronyms MOR, DOR and KOR are still widely used in the literature. The human N/OFQ receptor, NOP, is considered 'opioid-related' rather than opioid because, while it exhibits a high degree of structural homology with the conventional opioid receptors [304], it displays a distinct pharmacology. Currently there are numerous clinically used drugs, such as morphine and many other opioid analgesics, as well as antagonists such as naloxone. The majority of clinically used opiates are relatively selective μ agonists or partial agonists, though there are some μ/κ compounds, such as butorphanol, in clinical use. κ opioid agonists, such as the alkaloid nalfurafine and the peripherally acting peptide difelikefalin, are in clinical use for itch.

RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 ( CDK13 ) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.

Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated ‘ssGap-seq’, we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, RecA and SSB assembly profiles coincide globally, concentrated on the lagging strand and enhanced after UV irradiation. Unexpected results also abound. Near the terminus, RecA binding is favored over SSB, binding patterns change in the absence of RecG, and the absence of XerD results in massive RecA assembly. RecA may substitute for the absence of XerCD to resolve chromosome dimers. A RecA loading pathway may exist that is independent of RecBCD and RecFOR. Two prominent and focused peaks of RecA binding revealed a pair of 222 bp and GC-rich repeats, equidistant from dif and flanking the Ter domain. The repeats, here named RRS for replication risk sequence, trigger a genomically programmed generation of post-replication gaps that may play a special role in relieving topological stress during replication termination and chromosome segregation. As demonstrated here, ssGap-seq provides a new window on previously inaccessible aspects of ssDNA metabolism.

Planning for the impacts of climate change requires accurate projections by Earth system models (ESMs). ESMs, as developed by many research centres, estimate changes to weather and climate as atmospheric greenhouse gases (GHGs) rise, and they inform the influential Intergovernmental Panel on Climate Change (IPCC) reports. ESMs are advancing the understanding of key climate system attributes. However, there remain substantial inter-ESM differences in their estimates of future meteorological change, even for a common GHG trajectory, and such differences make adaptation planning difficult. Until recently, the primary approach to reducing projection uncertainty has been to place an emphasis on simulations that best describe the contemporary climate. Yet a model that performs well for present-day atmospheric GHG levels may not necessarily be accurate for higher GHG levels and vice versa. A relatively new approach of emergent constraints (ECs) is gaining much attention as a technique to remove uncertainty between climate models. This method involves searching for an inter-ESM link between a quantity that we can also measure now and a second quantity of major importance for describing future climate. Combining the contemporary measurement with this relationship refines the future projection. Identified ECs exist for thermal, hydrological and geochemical cycles of the climate system. As ECs grow in influence on climate policy, the method is under intense scrutiny, creating a requirement to understand them better. We hypothesise that as many Earth system components vary in both space and time, their behaviours often satisfy large-scale differential equations (DEs). Such DEs are valid at coarser scales than the equations coded in ESMs which capture finer high-resolution grid-box-scale effects. We suggest that many ECs link to such effective hidden DEs implicit in ESMs and that aggregate small-scale features. An EC may exist because its two quantities depend similarly on an ESM-specific internal bulk parameter in such a DE, with measurements constraining and revealing its (implicit) value. Alternatively, well-established process understanding coded at the ESM grid box scale, when aggregated, may generate a bulk parameter with a common “emergent” value across all ESMs. This single emerging parameter may link uncertainties in a contemporary climate driver to those of a climate-related property of interest. In these circumstances, the EC combined with a measurement of the driver that is uncertain constrains the estimate of the climate-related quantity. We offer simple illustrative examples of these concepts with generic DEs but with their solutions placed in a conceptual EC framework.

Reliable estimates of soil carbon change are required to determine the carbon budgets consistent with the Paris climate targets. This study evaluates projections of soil carbon during the 21st century in CMIP6 Earth System Models (ESMs) under a range of atmospheric composition scenarios. In general, we find a reduced spread of changes in global soil carbon (ΔCs) in CMIP6 compared to the previous CMIP5 model generation. However, similar reductions were not seen in the derived contributions to ΔCs due to both increases in plant Net Primary Productivity (NPP, named ΔCs,NPP) and reductions in the effective soil carbon turnover time (τs, named ΔCs,τ). Instead, we find a strong relationship across the CMIP6 models between these NPP and τs components of ΔCs, with more positive values of ΔCs,NPP being correlated with more negative values of ΔCs,τ. We show that this emergent relationship is the result of 'false priming', which leads to a decrease in the effective soil carbon turnover time as a direct result of NPP increase and occurs when the rate of increase of NPP is relatively fast compared to the slower timescales of a multipool soil carbon model. The inclusion of more soil carbon models with multiple pools in CMIP6 compared to CMIP5, therefore seems to have contributed towards the reduction in the overall model spread in future soil carbon projections.

BACKGROUND: Given the increasing complexities of the residency application processes, there is an ever-increasing need for faculty to serve in the role of fourth-year medical student career advisors. OBJECTIVE: This study aimed to investigate obstetrics and gynecology clerkship directors’ confidence and fulfillment with serving in the role of faculty career advisors. STUDY DESIGN: A 25-item electronic survey was developed and distributed to the 225 US obstetrics and gynecology clerkship directors in university-based and community-based medical schools with active memberships in the Association of Professors of Gynecology and Obstetrics. Items queried respondents on demographics, confidence in fourth-year advising, satisfaction with this aspect of their career, and resources used for advising. RESULTS: Of 225 clerkship directors, 143 (63.6%) responded to the survey. Nearly all clerkship directors (136/143 [95%]) reported advising fourth-year students. A median of 5.0 hours (interquartile range, 3.0–10.0) was spent per student in this advisory role, with 29 of 141 clerkship directors (20.5%) reporting some form of compensation for advising. Confidence in the ability to advise fourth-year medical students correlated significantly with number of years as a faculty, number of years as a clerkship director, and a higher full-time equivalent allotted as clerkship director. Fulfillment as a faculty career advisor was correlated with number of years as a clerkship director and a higher number of students advised. CONCLUSION: Obstetrics and gynecology clerkship directors regularly serve in the crucial role of faculty career advisor. Confidence in advising fourth-year students, advising fulfillment, and satisfaction with advising resources were all significantly correlated. We recommend that clerkship directors review resources available for advising and that they be provided academic time to serve as career advisors.

Early in the COVID-19 pandemic, demand for N95 respirators far exceeded the supply, leading to widespread shortages. Initially, the US Centers for Disease Control and Prevention did not recommend N95 respirators in nonhealthcare settings, in order to reserve them for healthcare workers. As N95s became more available, the recommendations were updated in May 2021 to include N95 respirators for nonhealthcare settings. In this study, we estimated the numbers of N95s needed for nonhealthcare essential workers in the United States. This information is valuable for crisis preparedness and planning for future large-scale communicable respiratory infectious disease epidemics or pandemics. We adapted a spreadsheet-based tool originally built to estimate the potential demand for N95 respirators during an influenza pandemic. We defined nonhealthcare essential occupations according to the 2020 US Department of Homeland Security guidance and used US Bureau of Labor Statistics employment numbers and Occupational Information Network data as model parameters. We modeled minimum, intermediate, and maximum N95 provision scenarios (as 1, 2, and 5 N95 respirators, respectively) per week per worker, for pandemic durations of 15 and 40 weeks. For 85.15 million nonhealthcare essential workers during a 15-week pandemic, an estimated 1.3 billion N95 respirators would be needed under minimum provision scenarios, 2.6 billion for intermediate provision, and 6.4 billion for maximum provision. During a 40-week pandemic, these estimates increased to 3.4 billion, 6.8 billion, and 17 billion. Public health authorities and policymakers can use these estimates when considering workplace respirator-wearing practices, including prioritization of allocation, for nonhealthcare essential workers. Our novel spreadsheet-based tool can also be used to quickly generate estimates of other preparedness and response equipment.

Background The number of primary and revision shoulder arthroplasties performed each year continues to increase. Relative value units (RVUs) are currently used by the Centers for Medicare and Medicaid Services (CMS) to determine physician reimbursement based on time, effort, and complexity of services rendered. Compared to primary shoulder arthroplasty, revision shoulder arthroplasties are often more technically challenging, have longer operative times, and pose a greater risk of intraoperative and postoperative complications. This study aims to compare surgeon reimbursement between primary and revision shoulder arthroplasty. Methods Utilizing a single institution shoulder arthroplasty database, we identified patients who underwent primary or revision shoulder arthroplasty between February 2011 and December 2013 by a single shoulder and elbow fellowship trained surgeon with over 20 years of experience at the time of data collection. The RVUs for primary and revision shoulder arthroplasty were obtained from the CMS Physician Fee schedule. Physician reimbursement for primary and revision shoulder arthroplasty was calculated using the CMS RVU to dollar conversion factor of $34.8921 per RVU. The RVU was divided by operative time to calculate an RVU/min for primary and revision shoulder arthroplasty. Monetary reimbursement per minute, case, day, and year was subsequently calculated. Results A total of 190 primary and 100 revision shoulder arthroplasties were performed during the study period. Mean RVU for primary shoulder arthroplasty was 22.13 ± 0.00 vs. 26.24 ± 1.10 for revision shoulder arthroplasty (P Conclusion While the RVU/case is higher for revision shoulder arthroplasty, the difference does not account for the additional operative time and complexity compared to primary shoulder arthroplasty. In light of this data, the current RVU reimbursement model should be reevaluated to account for these differences between primary and revision shoulder arthroplasty. Level of Evidence Level III; Retrospective Comparative Study