MarZIC: A Marginal Mediation Model for Zero-Inflated Compositional Mediators with Applications to Microbiome Data.

BACKGROUND: The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data and that the relative abundances have to sum to one. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are not zero (i.e., false zeros). METHODS: We develop a novel marginal mediation analysis method under the potential-outcomes framework to address the issues. We also show that the marginal model can account for the compositional structure of microbiome data. RESULTS: The mediation effect can be decomposed into two components that are inherent to the two-part nature of zero-inflated distributions. With probabilistic models to account for observing zeros, we also address the challenge with false zeros. A comprehensive simulation study and the application in a real microbiome study showcase our approach in comparison with existing approaches. CONCLUSIONS: When analyzing the zero-inflated microbiome composition as the mediators, MarZIC approach has better performance than standard causal mediation analysis approaches and existing competing approach.

Quantifying the population burden of musculoskeletal disorders, including impact on sickness absence: analysis of national Scottish data.

Objectives: Musculoskeletal disorders (MSDs) account for the greatest burden of years lived with disability globally. To prevent disability, good-quality services need to be commissioned, appropriate for local need. We analysed data collected systematically from a new musculoskeletal service serving 70% of the population of Scotland to evaluate: age- and sex-specific occurrence; anatomical distribution; and impact and effect on work ability. Methods: A new centralized telephone-based triage for people with musculoskeletal disorders was set up in Scotland in 2015. Available to most of the population aged >16 years (>3 million people), data were collected systematically into a database detailing: anatomical site, nature of onset, duration, impact/risk (modified STarT score), deprivation level and, for those in employment, sickness absence. Results: Data were available from 219 314 new callers, 2015-18. Calls were more frequently from women (60%), increased with age until the eighth decade, and 66% reported symptoms that had been present for >6 weeks. Callers were more likely to be living in more deprived areas in each age band between 20 and 64 years and tended to have higher-impact symptoms. The majority (53%) of callers were in employment, and 19% of these were off sick because of their symptoms. Sickness absence was more common among those with highest impact/risk scores from deprived areas with more acute symptoms. Discussion: Large-scale systematic data collection for MSDs emphasizes the size and impact of the burden among adults aged >16 years. A socio-economic gradient is evident in terms of prevalence and impact of MSDs, particularly for sickness absence.

Increased DNA methylation, cellular senescence and premature epigenetic aging in guinea pigs and humans with tuberculosis.

BACKGROUND: Tuberculosis (TB) is the archetypical chronic infection, with patients having months of symptoms before diagnosis. In the two years after successful therapy, survivors of TB have a three-fold increased risk of death. METHODS: Guinea pigs were infected with Mycobacterium tuberculosis (Mtb) for 45 days, followed by RRBS DNA methylation analysis. In humans, network analysis of differentially expressed genes across three TB cohorts were visualized at the pathway-level. Serum levels of inflammation were measured by ELISA. Horvath (DNA methylation) and RNA-seq biological clocks were used to investigate shifts in chronological age among humans with TB. RESULTS: Guinea pigs with TB demonstrated DNA hypermethylation and showed system-level similarity to humans with TB (p-value = 0.002). The transcriptome in TB in multiple cohorts was enriched for DNA methylation and cellular senescence. Senescence associated proteins CXCL9, CXCL10, and TNF were elevated in TB patients compared to healthy controls. Humans with TB demonstrate 12.7 years (95% CI: 7.5, 21.9) and 14.38 years (95% CI: 10.23-18.53) of cellular aging as measured by epigenetic and gene expression based cellular clocks, respectively. CONCLUSIONS: In both guinea pigs and humans, TB perturbs epigenetic processes, promoting premature cellular aging and inflammation, a plausible means to explain the long-term detrimental health outcomes after TB.

Implementation of collaborative care for depressive disorder treatment among accountable care organizations.

ABSTRACT: Collaborative care - primary care models combining care management, consulting behavioral health clinicians, and registries to target mental health treatment - is a cost-effective depression treatment model, but little is known about uptake of collaborative care in a national setting. Alternative payment models such as accountable care organizations (ACOs), in which ACOs are responsible for quality and cost for defined patient populations, may encourage collaborative care use.Determine prevalence of collaborative care implementation among ACOs and whether ACO structure or contract characteristics are associated with implementation.Cross-sectional analysis of 2017-2018 National Survey of ACOs (NSACO). Overall, 55% of ACOs returned a survey (69% of Medicare, 36% of non-Medicare ACOs); 48% completed at least half of core survey questions. We used logistic regression to examine the association between implementation of core collaborative care components - care management, a consulting mental health clinician, and a patient registry to track mental health symptoms - and ACO characteristics.Four hundred five National Survey of ACOs respondents answering questions on collaborative care implementation.Only 17% of ACOs reported implementing all collaborative care components. Most reported using care managers (71%) and consulting mental health clinicians (58%), =just 26% reported using patient registries. After adjusting for multiple ACO characteristics, ACOs responsible for mental health care quality measures were 15 percentage points (95% CI 5-23) more likely to implement collaborative care.Most ACOs are not utilizing behavioral health collaborative care. Including mental health care quality measures in payment contracts may facilitate implementation of this cost-effective model. Improving provider capacity to track and target depression treatment with patient registries is warranted as payment contracts focus on treatment outcomes.

A New Standard for Advance Care Planning (ACP) Conversations in the Hospital: Results from a Delphi Panel.

BACKGROUND: Fewer than half of the US population has an advance healthcare directive. Hospitalizations offer a key opportunity for clinicians to engage patients in advance care planning (ACP) conversations. Guidelines suggest screening for the presence of "serious illness" but do not further specify how to prioritize the 12.4 million patients hospitalized each year. OBJECTIVE: To establish a normative standard for prioritizing hospitalized patients for ACP conversations. DESIGN AND SETTING: A modified Delphi study, with three iterative rounds of online surveys. PARTICIPANTS: Multi-disciplinary group of US-based clinicians with research and practical expertise in ACP. MAIN MEASURES: Indirect and direct elicitation of short-term and 1-year risk of mortality that prompt experts to prioritize ACP conversations for hospitalized adults. MAIN RESULTS: Fifty-seven of 108 (52%) candidate panelists completed round 1, and 47 completed rounds 2 and 3. Panelists were primarily physicians (84%), with significant experience (mean years 23 [SD 9.8]), who either taught (55%) and/or performed research about ACP (55%). In round 1, > 70% of panelists agreed that all hospitalized adults ≥ 65 years should have an ACP conversation before discharge, but disagreed about the timing and content of the conversation. By round 3, > 70% of participants agreed that patients with either high (> 10%) short-term or high (≥ 34%) 1-year risk of mortality should have a goals of care conversation (i.e., focused on preferences for near-term treatment), while patients with low (≤ 10%) short-term and low (< 19%) 1-year risk of mortality warranted an ACP conversation (i.e., focused on preferences for future care) before discharge. LIMITATIONS: Use of case vignettes to elicit clinician judgment; response rate. CONCLUSIONS: Panelists agreed that clinicians should have an ACP conversation with all hospitalized adults over 65 years in an ACP conversation, adjusting the content and timing of the conversation conditional on the patient's risk of short-term and 1-year mortality.

Graph literacy matters: Examining the association between graph literacy, health literacy, and numeracy in a Medicaid eligible population.

OBJECTIVES: Graphic display formats are often used to enhance health information. Yet limited attention has been paid to graph literacy in people of lower education and lower socioeconomic status (SES). This study aimed to: 1) examine the relationship between graph literacy, numeracy, health literacy and sociodemographic characteristics in a Medicaid-eligible population 2) determine the impact of graph literacy on comprehension and preference for different visual formats. METHODS: We conducted a cross-sectional online survey among people in the US on Medicaid, and of presumed lower education and SES. RESULTS: The mean graph literacy score among 436 participants was 1.47 (SD 1.05, range: 0 to 4). Only graph literacy was significantly associated with overall comprehension (p < .001). Mean comprehension scores were highest for the table format (1.91), closely followed by bar graph (1.85) and icon array (1.80). Information comprehension was aligned with preference scores. CONCLUSIONS: Graph literacy in a Medicaid-eligible population was lower than previous estimates in the US. Tables were better understood, with icon arrays yielding the lowest score. Preferences aligned with comprehension. PRACTICE IMPLICATIONS: It may be necessary to reconsider the use of graphic display formats when designing information for people with lower educational levels. Further research is needed.

Regulation of stem cell function and neuronal differentiation by HERV-K via mTOR pathway.

Stem cells are capable of unlimited proliferation but can be induced to form brain cells. Factors that specifically regulate human development are poorly understood. We found that human stem cells expressed high levels of the envelope protein of an endogenized human-specific retrovirus (HERV-K, HML-2) from loci in chromosomes 12 and 19. The envelope protein was expressed on the cell membrane of the stem cells and was critical in maintaining the stemness via interactions with CD98HC, leading to triggering of human-specific signaling pathways involving mammalian target of rapamycin (mTOR) and lysophosphatidylcholine acyltransferase (LPCAT1)-mediated epigenetic changes. Down-regulation or epigenetic silencing of HML-2 env resulted in dissociation of the stem cell colonies and enhanced differentiation along neuronal pathways. Thus HML-2 regulation is critical for human embryonic and neurodevelopment, while it's dysregulation may play a role in tumorigenesis and neurodegeneration.

KMN-159, a novel EP4 receptor selective agonist, stimulates osteoblastic differentiation in cultured whole rat bone marrow.

KMN-159 is the lead compound from a series of novel difluorolactam prostanoid EP4 receptor agonists aimed at inducing local bone formation while avoiding the inherent side effects of systemic EP4 activation. KMN-159 is a potent, selective small molecule possessing pharmacokinetic properties amenable to local administration. Unfractionated rat bone marrow cells (BMCs) were treated once at plating with escalating doses of KMN-159 (1 pM to 10 µM). The resulting elevated alkaline phosphatase (ALP) levels measured 9 days post-dose are consistent with increased osteoblastic differentiation and exposure to KMN-159 at low nanomolar concentrations for as little as 30 min was sufficient to induce complete osteoblast differentiation of the BMCs from both sexes and regardless of age. ALP induction was blocked by an EP4 receptor antagonist but not by EP1 or EP2 receptor antagonists and was not induced by EP2 or EP3 receptor agonists. Addition of BMCs to plates coated with KMN-159 24 days earlier resulted in ALP activation, highlighting the chemical stability of the compound. The expression of phenotype markers such as ALP, type I collagen, and osteocalcin was significantly elevated throughout the osteoblastic differentiation timecourse initiated by KMN-159 stimulation. An increased number of tartrate-resistant acid phosphatase-positive cells was observed KMN-159 or PGE2 treated BMCs but only in the presence of exogenous receptor activator of nuclear factor kappa-Β ligand (RANKL). No change in the number of adipocytes was observed. KMN-159 also increased bone healing in a rat calvarial defect model with a healing rate equivalent to recombinant human bone morphogenetic protein-2. Our studies show that KMN-159 is able to stimulate osteoblastic differentiation with a very short time of exposure, supporting its potential as a therapeutic candidate for augmenting bone mass.

Difluoromethylene at the γ-Lactam α-Position Improves 11-Deoxy-8-aza-PGE1 Series EP4 Receptor Binding and Activity: 11-Deoxy-10,10-difluoro-8-aza-PGE1 Analog (KMN-159) as a Potent EP4 Agonist.

A series of small-molecule full agonists of the prostaglandin E2 type 4 (EP4) receptor have been generated and evaluated for binding affinity and cellular potency. KMN-80 and its gem-difluoro analog KMN-159 possess high selectivity relative to other prostanoid receptors. Difluoro substitution is positioned alpha to the lactam ring carbonyl and results in KMN-159's fivefold increase in potency versus KMN-80. The two analogs exhibit electronic and conformational variations, including altered nitrogen hybridization and lactam ring puckering, that may drive the observed difluoro-associated increased potency within this four-compound series.

The Vegetation Red Edge Biosignature Through Time on Earth and Exoplanets.

The high reflection of land vegetation in the near-infrared, the vegetation red edge (VRE), is often cited as a spectral biosignature for surface vegetation on exoplanets. The VRE involves only a few percentage change in reflectivity for a disk-integrated observation of present-day Earth. Here we show that the strength of Earth's VRE has increased over the past ∼500 million years of land plant evolution and may continue to increase as solar luminosity increases and the planet warms, until either vegetation coverage is reduced, or the planet's atmosphere becomes opaque to light reflected off the surface. Early plants such as mosses and liverworts, which dominated the land 500-400 million years ago, produce a weaker VRE, approximately half as strong as that of modern vegetation. We explore how the changes in land plants, as well as geological changes such as ice coverage during ice ages and interglacial periods, influence the detectability of the VRE through Earth's geological past. Our results show that the VRE has varied through the evolutionary history of land plants on Earth and could continue to change into the future if hotter climate conditions became dominant, encouraging the spread of vegetation. Our findings suggest that older and hotter Earth-like planets are good targets for the search for a VRE signature. In addition, hot exoplanets and dry exoplanets with some water could be the best targets for a successful vegetation biosignature detection. As well as a strong red edge, lower cloud fractions and low levels of atmospheric water vapor on such planets could make it easier to detect surface features in general.

Habitability: A Review.

Habitability is a widely used word in the geoscience, planetary science, and astrobiology literature, but what does it mean? In this review on habitability, we define it as the ability of an environment to support the activity of at least one known organism. We adopt a binary definition of "habitability" and a "habitable environment." An environment either can or cannot sustain a given organism. However, environments such as entire planets might be capable of supporting more or less species diversity or biomass compared with that of Earth. A clarity in understanding habitability can be obtained by defining instantaneous habitability as the conditions at any given time in a given environment required to sustain the activity of at least one known organism, and continuous planetary habitability as the capacity of a planetary body to sustain habitable conditions on some areas of its surface or within its interior over geological timescales. We also distinguish between surface liquid water worlds (such as Earth) that can sustain liquid water on their surfaces and interior liquid water worlds, such as icy moons and terrestrial-type rocky planets with liquid water only in their interiors. This distinction is important since, while the former can potentially sustain habitable conditions for oxygenic photosynthesis that leads to the rise of atmospheric oxygen and potentially complex multicellularity and intelligence over geological timescales, the latter are unlikely to. Habitable environments do not need to contain life. Although the decoupling of habitability and the presence of life may be rare on Earth, it may be important for understanding the habitability of other planetary bodies.

In search of future earths: assessing the possibility of finding Earth analogues in the later stages of their habitable lifetimes.

Earth will become uninhabitable within 2-3 Gyr as a result of the increasing luminosity of the Sun changing the boundaries of the habitable zone (HZ). Predictions about the future of habitable conditions on Earth include declining species diversity and habitat extent, ocean loss, and changes to geochemical cycles. Testing these predictions is difficult, but the discovery of a planet that is an analogue to future Earth could provide the means to test them. This planet would need to have an Earth-like biosphere history and to be approaching the inner edge of the HZ at present. Here, we assess the possibility of finding such a planet and discuss the benefits of analyzing older Earths. Finding an old-Earth analogue in nearby star systems would be ideal, because this would allow for atmospheric characterization. Hence, as an illustrative example, G stars within 10 pc of the Sun are assessed as potential old-Earth-analog hosts. Six of these represent good potential hosts. For each system, a hypothetical Earth analogue is placed at locations within the continuously habitable zone (CHZ) that would allow enough time for Earth-like biosphere development. Surface temperature evolution over the host star's main sequence lifetime (assessed by using a simple climate model) is used to determine whether the planet would be in the right stage of its late-habitable lifetime to exhibit detectable biosignatures. The best candidate, in terms of the chances of planet formation in the CHZ and of biosignature detection, is 61 Virginis. However, planet formation studies suggest that only a small fraction (0.36%) of G stars in the solar neighborhood could host an old-Earth analogue. If the development of Earth-like biospheres is rare, requiring a sequence of low-probability events to occur, biosphere evolution models suggest they are rarer still, with only thousands being present in the Galaxy as a whole.

Factors associated with geographic variation in cost per episode of care for three medical conditions.

OBJECTIVE: To identify associations between market factors, especially relative reimbursement rates, and the probability of surgery and cost per episode for three medical conditions (cataract, benign prostatic neoplasm, and knee degeneration) with multiple treatment options. METHODS: We use 2004-2006 Medicare claims data for elderly beneficiaries from sixty nationally representative communities to estimate multivariate models for the probability of surgery and cost per episode of care as a function local market factors, including Medicare physician reimbursement for surgical versus non-surgical treatment and the availability of primary care and specialty physicians. We used Symmetry's Episode Treatment Groups (ETG) software to group claims into episodes for the three conditions (n = 540,874 episodes). RESULTS: Higher Medicare reimbursement for surgical episodes and greater availability of the relevant specialists are significantly associated with more surgery and higher cost per episode for all three conditions, while greater availability of primary care physicians is significantly associated with less frequent surgery and lower cost per episode. CONCLUSION: Relative Medicare reimbursement rates for surgical vs. non-surgical treatments and the availability of both primary care physicians and relevant specialists are associated with the likelihood of surgery and cost per episode.

Increased use of the emergency department after health care reform in Massachusetts.

STUDY OBJECTIVE: With implementation of the Patient Protection and Affordable Care Act, 30 million individuals are predicted to gain access to health insurance. The experience in Massachusetts, which implemented a similar reform beginning in 2006, should provide important lessons about the effect of health care reform on emergency department (ED) utilization. Our objective is to understand the extent to which Massachusetts health care reform was associated with changes in ED utilization. METHODS: We compared changes in ED utilization at the population level for individuals from areas of the state that were affected minimally by health care reform with those from areas that were affected the most, as well as for those younger than 65 years and aged 65 years or older. We used a difference-in-differences identification strategy to compare rates of ED visits in the prereform period, during the reform, and in the postreform period. Because we did not have population-level data on insurance status, we estimated area-level insurance rates by using the percentage of actual visits made during each period by individuals with insurance. RESULTS: We studied 13.3 million ED visits during 2004 to 2009. Increasing insurance coverage in Massachusetts was associated with increasing use of the ED; these results were consistent across all specifications, including the younger than 65 years versus aged 65 years or older comparison. Depending on the model used, the implementation of health care reform was estimated to result in an increase in ED visits per year of between 0.2% and 1.2% within reform and 0.2% and 2.2% postreform compared with the prereform period. CONCLUSION: The implementation of health care reform in Massachusetts was associated with a small but consistent increase in the use of the ED across the state. Whether this was due to the elimination of financial barriers to seeking care in the ED, a persistent shortage in access to primary care for those with insurance, or some other cause is not entirely clear and will need to be addressed in future research.

High-resolution analysis with novel cell-surface markers identifies routes to iPS cells.

The generation of induced pluripotent stem (iPS) cells presents a challenge to normal developmental processes. The low efficiency and heterogeneity of most methods have hindered understanding of the precise molecular mechanisms promoting, and roadblocks preventing, efficient reprogramming. Although several intermediate populations have been described, it has proved difficult to characterize the rare, asynchronous transition from these intermediate stages to iPS cells. The rapid expansion of minor reprogrammed cells in the heterogeneous population can also obscure investigation of relevant transition processes. Understanding the biological mechanisms essential for successful iPS cell generation requires both accurate capture of cells undergoing the reprogramming process and identification of the associated global gene expression changes. Here we demonstrate that in mouse embryonic fibroblasts, reprogramming follows an orderly sequence of stage transitions, marked by changes in the cell-surface markers CD44 and ICAM1, and a Nanog-enhanced green fluorescent protein (Nanog-eGFP) reporter. RNA-sequencing analysis of these populations demonstrates two waves of pluripotency gene upregulation, and unexpectedly, transient upregulation of several epidermis-related genes, demonstrating that reprogramming is not simply the reversal of the normal developmental processes. This novel high-resolution analysis enables the construction of a detailed reprogramming route map, and the improved understanding of the reprogramming process will lead to new reprogramming strategies.

From cytoplasm to environment: the inorganic ingredients for the origin of life.

Early in its history, Earth's surface developed from an uninhabitable magma ocean to a place where life could emerge. The first organisms, lacking ion transporters, fixed the composition of their cradle environment in their intracellular fluid. Later, though life adapted and spread, it preserved some qualities of its initial environment within. Modern prokaryotes could thus provide insights into the conditions of early Earth and the requirements for the emergence of life. In this work, we constrain Earth's life-forming environment through detailed analysis of prokaryotic intracellular fluid. Rigorous assessment of the constraints placed on the early Earth environment by intracellular liquid will provide insight into the conditions of abiogenesis, with implications not only for our understanding of early Earth but also the formation of life elsewhere in the Universe.

Transcriptional activation by Oct4 is sufficient for the maintenance and induction of pluripotency.

Oct4 is an essential regulator of pluripotency in vivo and in vitro in embryonic stem cells, as well as a key mediator of the reprogramming of somatic cells into induced pluripotent stem cells. It is not known whether activation and/or repression of specific genes by Oct4 is relevant to these functions. Here, we show that fusion proteins containing the coding sequence of Oct4 or Xlpou91 (the Xenopus homolog of Oct4) fused to activating regions, but not those fused to repressing regions, behave as Oct4, suppressing differentiation and promoting maintenance of undifferentiated phenotypes in vivo and in vitro. An Oct4 activation domain fusion supported embryonic stem cell self-renewal in vitro at lower concentrations than that required for Oct4 while alleviating the ordinary requirement for the cytokine LIF. At still lower levels of the fusion, LIF dependence was restored. We conclude that the necessary and sufficient function of Oct4 in promoting pluripotency is to activate specific target genes.

Life and light: exotic photosynthesis in binary and multiple-star systems.

The potential for Earth-like planets within binary/multiple-star systems to host photosynthetic life was evaluated by modeling the levels of photosynthetically active radiation (PAR) such planets receive. Combinations of M and G stars in (i) close-binary systems; (ii) wide-binary systems, and (iii) three-star systems were investigated, and a range of stable radiation environments were found to be possible. These environmental conditions allow for the possibility of familiar, but also more exotic, forms of photosynthetic life, such as IR photosynthesizers and organisms that are specialized for specific spectral niches.

Physician patient-sharing networks and the cost and intensity of care in US hospitals.

BACKGROUND: There is substantial variation in the cost and intensity of care delivered by US hospitals. We assessed how the structure of patient-sharing networks of physicians affiliated with hospitals might contribute to this variation. METHODS: We constructed hospital-based professional networks based on patient-sharing ties among 61,461 physicians affiliated with 528 hospitals in 51 hospital referral regions in the US using Medicare data on clinical encounters during 2006. We estimated linear regression models to assess the relationship between measures of hospital network structure and hospital measures of spending and care intensity in the last 2 years of life. RESULTS: The typical physician in an average-sized urban hospital was connected to 187 other doctors for every 100 Medicare patients shared with other doctors. For the average-sized urban hospital an increase of 1 standard deviation (SD) in the median number of connections per physician was associated with a 17.8% increase in total spending, in addition to 17.4% more hospital days, and 23.8% more physician visits (all P<0.001). In addition, higher "centrality" of primary care providers within these hospital networks was associated with 14.7% fewer medical specialist visits (P<0.001) and lower spending on imaging and tests (-9.2% and -12.9% for 1 SD increase in centrality, P<0.001). CONCLUSIONS: Hospital-based physician network structure has a significant relationship with an institution's care patterns for their patients. Hospitals with doctors who have higher numbers of connections have higher costs and more intensive care, and hospitals with primary care-centered networks have lower costs and care intensity.