A meta-analysis of the carcinogenic effects of particulate matter and polycyclic aromatic hydrocarbons

Urbanization has numerous benefits to human society, but some aspects of urban environments, such as air pollution, can negatively affect human health. Two major air pollutants, particulate matter (PM) and polycyclic aromatic hydrocarbons (PAH), have been classified as carcinogens by the International Agency for Research on Cancer. Here, we answer two questions: (1) What are the carcinogenic effects of PM and PAH exposure? (2) How does carcinogenic risk vary across geographical regions? We performed a comprehensive literature search of peer-reviewed published studies examining the link between air pollution and human cancer rates. Focusing on studies published since 2014 when the last IARC monograph on air pollution was published, we converted the extracted data into relative risks and performed subgroup analyses. Exposure to PM2.5 (per 10μg/m3) resulted in an 8.5% increase in cancer incidence when all cancer types were combined, and risk for individual cancer types (i.e. lung cancer and adenocarcinoma) was also elevated. PM2.5 was also associated with 2.5% higher mortality due to cancer when all types of cancer were combined, and for individual cancer types (i.e., lung and breast cancer). Exposure to PM2.5 and PM10 posed the greatest risk to lung cancer incidence and mortality in Europe (PM2.5 RR 2.15; PM10 RR 1.26); the risk in Asia and the Americas was also elevated. Exposure to PAH and benzo[a]pyrene significantly increased the pooled risk of cancer incidence (10.8% and 8.0% respectively) at the highest percentile of exposure concentration. Our meta-analyses of studies over the past decade shows that urban air pollution in the form of PM2.5, PM10, and PAH all elevate the incidence and mortality of cancer. We discuss the possible mechanisms of carcinogenesis of PM and PAH. These results support World Health Organization's conclusion that air pollution poses among the greatest health risks to humans living in cities.

Impact of Giving Patients Your Personal Phone Number in Otolaryngology-Head & Neck Surgery

OBJECTIVE

Patient-provider communication is a major barrier to care, with some providers giving their personal phone number (PPN) to patients for increased accessibility. We investigated participant utilization of provider's PPN, its effect on participant satisfaction, provider's ability to predict abuse of this practice, and evolving provider perceptions.

STUDY DESIGN

Prospective, randomized study.

SETTING

Single institution, tertiary referral center.

METHODS

During a 2-week period, otolaryngology patients were randomized to either receive their provider's PPN or not. Providers predicted the likelihood of abuse. All calls/texts were documented for 4 weeks. At the study's conclusion, participants were surveyed using Press Ganey metrics. Providers were surveyed before and after to assess their likelihood of providing patients with their PPN and its impact on work demands.

RESULTS

Of the 507 participants enrolled, 266 were randomized to the phone number group (+PN). Of 44 calls/texts from 24 participants, 8 were considered inappropriate. Ten participants were predicted to abuse the PPN, but only one was accurately identified. Participants in the +PN group had a greater mean composite satisfaction score than the control group (4.8 vs 4.3; Welch's t-test, P < .0011). At the conclusion of the study, providers were more likely to share their PPN (Wilcoxon signed-rank test, P < .0313), and their perceived impact of this practice on workload was lower (Wilcoxon signed-rank test, P < .0469).

CONCLUSION

This study demonstrates low patient utilization of provider PPNs, and poor provider predictive ability of patient abuse. Receipt of provider's PPN was associated with improved patient satisfaction.

Vasculitis and Kidney Disease

Pediatric vasculitis is a complex group of disorders that commonly presents with multisystem involvement. Renal vasculitis can be isolated to the kidneys or can occur as part of a broader multiorgan vasculitis. Depending on severity, renal vasculitis may present as acute glomerulonephritis (AGN) often associated with hypertension and sometimes with a rapidly deteriorating clinical course. Prompt diagnosis and initiation of therapy are key to preserving kidney function and preventing long-term morbidity and mortality. This review focuses on the clinical presentation, diagnosis, and treatment objectives for common forms of renal vasculitis seen in pediatric patients.

Natural and human factors influencing urban particulate matter concentrations in central heating areas with long-term wearable monitoring devices

In northern China, central heating, as an important source of urban particulate matter (UPM), causes more than half of the air pollution during the heating season and has significant spatial-temporal heterogeneity. Owing to the limitations of stationary air monitoring networks, few studies distinguish between heating/non-heating seasons and few have been conducted in urban areas. However, fixed monitoring cannot accurately capture the dynamic exposure of residents to UPM, and there is a lack of comprehensive evaluation of the factors affecting UPM. Therefore, this study used wearable Sniffer 4D equipment to monitor the concentrations of UPM (PM₁, PM_2.5, and PM₁₀) in selected typical areas of Shenyang City from March 2019 to February 2020. A random forest model was combined with land use and point-of-interest data to analyze the contributions and marginal effects of multiple influences on UPM, in both heating and non-heating seasons. The results showed that in the eastern part of the study area, UPM showed completely opposite spatial distribution characteristics during the two seasons. The concentrations of UPM were higher during the heating season than during the non-heating season. The results indicated that temperature and humidity were important factors in diffusing UPM. The production and operation of boilers were important for the production of UPM. In two-dimensional landscape pattern indices, the percentage of forest and Shannon diversity index were the first and second most important factors, respectively. The three-dimensional pattern of buildings had important effects on the transport and diffusion of UPM (landscape height range >100, floor area ratio >1.3, and landscape volume density >5). Wearable devices could monitor the real situation of residents' exposure to UPM and quantify the factors influencing the spatial-temporal distribution of UPM in an ecological sense. These results provide a scientific basis for urban planning and for health risk reduction for residents.

Systemic corticosteroids for orbital complications of pediatric rhinosinusitis: A systematic review

OBJECTIVES

Determine if systemic corticosteroids administration is associated with reduced length of stay, surgical intervention, and abscess formation in pediatric patients with orbital complications of rhinosinusitis.

METHODS

Systematic review and meta-analysis were performed utilizing the PubMed and MEDLINE databases to identify articles published between January 1990 and April 2020. Retrospective cohort study of the same patient population over the same time period at our institution.

RESULTS

Eight studies, 477 individuals, met criteria for inclusion in the systematic review. 144 patients (30.2%) received systemic corticosteroids, while 333 patients (69.8%) did not. Meta-analyses of frequency of surgical intervention and subperiosteal abscess showed no difference between those who did and did not receive systemic steroids ([OR = 1.06; 95% CI: 0.46 to 2.48] and [OR = 1.08; 95% CI: 0.43 to 2.76], respectively). 6 articles evaluated hospital length of stay (LOS). 3 of these reported enough data to perform meta-analysis, which showed patients with orbital complications who received systemic corticosteroids had shorter mean hospital LOS when compared with those who did not receive systemic steroids (SMD = -2.92, 95% CI: 5.65 to -0.19).

CONCLUSION

While available literature was limited, systematic review and meta-analysis suggests systemic corticosteroids decrease length of stay for hospitalized pediatric patients with orbital complications of sinusitis. Further research is needed to more clearly define the role of systemic corticosteroids as an adjunctive treatment.

Green areas and students' academic performance in the Federal District, Brazil: An assessment of three greenness metrics

Most of the epidemiological investigations looking at the health benefits of green spaces have measured the level of green areas by using only one approach, mainly the Normalized Difference Index - NDVI (a satellite-derived indicator). We hypothesized a difference in the association between health and green space depending on the metric used to measure green exposure. This study considers students' academic performance as a proxy of cognitive abilities (a health indicator). We estimated the relationship between green areas and students' academic performance in the Federal District (FD), Brazil, with three different greenness metrics: NDVI, distance to green spaces (m) - obtained from land use data, and quantity of green spaces (m²) - also from land use data. We assessed student-level academic performance data provided by the Department of the Education in the FD. The data includes students from the public schools in the FD for 256 schools (all the public schools in the FD) and 344,175 students (all the students enrolled in the public schools in the FD in 2017-2020).). For the first metric represented by the distance to green spaces, we estimated the straight-line distance between each school and the nearest green area. For NDVI and quantity of green spaces, we estimated the area of all green spaces within buffers of 500 m, 750 m, and 1 km around the schools. We applied a cross-sectional study design using mixed-effects regression models to analyze the association exposure to green areas around schools and student-level academic performance. Our results confirmed our hypothesis showing that the impact of green areas on students' performance varied significantly depending on the type of green metric. After adjustments for the covariates, we estimated that NDVI is positively associated with school-level academic performance, with an estimated coefficient of 0.91 (95%CI: 0.83; 0.99) for NDVI values at a school's centroid. Distance to green areas was negatively associated with academic performance [-2.09 × 10^-5 (95CI: 3.91 × 10^-5; -2.84 × 10^-6]. The quantity of green areas was estimated with mixed results (direction of the association), depending on the buffer size. Results from this paper suggest that epidemiological investigations must consider the different effects of greenness measures when looking at the association between green space and academic performance. More studies on residual confounding from this association with a different study design are needed to promote public health by making schools healthier.

Birth weight following pregnancy wildfire smoke exposure in more than 1.5 million newborns in Brazil: A nationwide case-control study

Background

Air pollution exposure has been associated with critical neonatal morbidities, including low birth weight (LBW). However, little is known on short-term exposure to wildfire smoke and LBW. In this study, we estimated the association between birth weight following pregnancy and wildfire smoke exposure in more than 1.5 million newborns in Brazil (considered as a very fire-prone region worldwide).

Methods

We applied a logistic regression model to estimate the percent variation in newborns with low birth weight when exposed to wildfire in different trimesters of the pregnancy.

Findings

After adjusting the model with relevant covariates, we found that an increase of 100 wildfire records in Brazil was associated with an increase in low birth weight in the Midwest region [0.98% (95%CI:0.34; 1.63)] and in the South region [18.55% (95%CI:13.66; 23.65)] when the exposure occurred in the first trimester of pregnancy.

Interpretation

Wildfires were associated with LBW and this should be of public health concern for policymakers.

Funding

Brazilian Agencies National Council for Scientific and Technological Development (CNPq); Ministry of Science, Technology and Innovation in Brazil (MCTI); and Novo Nordisk Foundation Challenge Programme.

Impact of Liposomal Bupivacaine on Post-Operative Pain and Opioid Usage in Thyroidectomy

OBJECTIVES

Opioid analgesia has been integral in post-operative pain control for decades. The over-prescription of opioids, commonly in the surgical patient, has contributed to the current opioid epidemic. Liposomal bupivacaine (LB), a long-acting analgesia formulation, has demonstrated decreased post-operative pain and opioid requirements in patients treated across multiple surgical subspecialties. The aims of this retrospective study are to assess post-operative pain and opioid use in patients who received LB at the time of thyroidectomy.

METHODS

A cohort-matched retrospective review of patients who underwent thyroidectomy by 2 surgeons between January 2010 and December 2019 was performed. Patients were divided into those that received LB intraoperatively and those that did not. Statistical analyses were performed using the Chi-square or Fisher's exact test, and 2-sample T-test or Wilcoxon rank sum test.

RESULTS

Of the 201 patients included in this study, 113 patients received LB and 88 did not. Patients who received LB had a lower median visual analog scale (VAS) pain score (2 vs 3, P = .2252), lower maximum VAS pain score (6 vs 7, P = .0898), were less likely to require opioid medications (73.5% vs 85.2%, P = .0434), and had a lower percentage of daily morphine milligram equivalent value ≥45 (89.8% vs 95.3%, P = .1581) during the post-operative period when compared to those that did not.

CONCLUSION

This study suggests a role for incisional infiltration with LB for post-operative pain management in patients undergoing transcervical thyroidectomy. We report reduced post-operative pain scores and opioid analgesia requirements in patients who received LB.

Global COVID-19 lockdown highlights humans as both threats and custodians of the environment

The global lockdown to mitigate COVID-19 pandemic health risks has altered human interactions with nature. Here, we report immediate impacts of changes in human activities on wildlife and environmental threats during the early lockdown months of 2020, based on 877 qualitative reports and 332 quantitative assessments from 89 different studies. Hundreds of reports of unusual species observations from around the world suggest that animals quickly responded to the reductions in human presence. However, negative effects of lockdown on conservation also emerged, as confinement resulted in some park officials being unable to perform conservation, restoration and enforcement tasks, resulting in local increases in illegal activities such as hunting. Overall, there is a complex mixture of positive and negative effects of the pandemic lockdown on nature, all of which have the potential to lead to cascading responses which in turn impact wildlife and nature conservation. While the net effect of the lockdown will need to be assessed over years as data becomes available and persistent effects emerge, immediate responses were detected across the world. Thus, initial qualitative and quantitative data arising from this serendipitous global quasi-experimental perturbation highlights the dual role that humans play in threatening and protecting species and ecosystems. Pathways to favorably tilt this delicate balance include reducing impacts and increasing conservation effectiveness.

Antiretroviral Laboratory Monitoring and Implications for HIV Clinical Care in the Era of COVID-19 and Beyond

In the era of COVID-19, providers are delaying laboratory testing in people with HIV (PWH). The purpose of this study was to examine the clinical significance of renal, liver, and lipid testing. We reviewed the charts of 261 PWH who initiated care at an academic HIV clinic between January 1, 2016 and December 21, 2018. Analysis included one-sided binomial exact tests and multiple linear, Poisson, and Beta regression models. The most common abnormality was a glomerular filtration rate (GFR) <60 mL/min (10%). Age <40 years [estimated relative rate (rr) 0.017, 95% confidence interval (CI) 0.207 to 0.494], cobicistat (rr 0.284, 95% CI 0.128 to 0.63), and tenofovir alafenamide (rr 0.295 95% CI 0.151 to 0.573) were associated with a decreased risk of GFR <60 mL/min. An increased AST and ALT ≥2 × upper limit of normal (ULN) was found in 5% and 3%, respectively. Hepatitis C and use of darunavir and lopinavir were associated with increased AST or ALT. When a GFR was <60 mL/min or an AST or ALT was ≥2 × ULN, no action was taken in 53% of cases. In 18% of cases the only intervention was repeat testing. The most common interventions after lipid results were calculation of a 10-year cardiovascular risk score (31%) and addition of a statin (18%). Taking action after lipid results was strongly associated with age ≥40 (rr 7.37, 95% CI 3.0 to 18.3). Young PWH without hepatitis C rarely have renal, liver, or lipid test results that alter clinical care. Decreased testing should be considered.

Associations between socioeconomic status and ultrafine particulate exposure in the school commute: An environmental inequality study for Toronto, Canada

Ultrafine particulate matter (UFP) air pollution is unevenly distributed across urban environments. Disparities in routine activity patterns, such as the exposure risk we face at work or on the commute, can contribute to chronic exposure-related health outcomes that place excess burdening on vulnerable population groups. In Canada, there is disagreement in the literature on the nature of these exposure-related inequalities, and our understanding of disparities associated with specific activity patterns such as commuting is limited. In the context of UFP specific exposure, these relationships are almost entirely unexplored in the environmental inequality literature. Our study presents an exploratory analysis of UFP exposure patterns in Toronto, Canada. We examined UFP dosage disparities experienced by children during routine school commutes. We estimated single trip dosages that accounted for variation in ambient UFP concentration, route morphology (distance, slope) and their effect on inhalation rate and trip duration. We aggregated these values at the dissemination-area level and collected socioeconomic status descriptors from the 2016 census. Our OLS model showed significant spatial autocorrelation (MI = 0.59, p < 0.001), and we instead applied a spatial error model to account for spatial effects in our dataset. We identified significant associations related to median income (β = -0.087, p < 0.05), government transfer dependence (β = -0.107, p < 0.005), immigration status (β = 0.119, p < 0.001), and education rates (β = -0.059, p < 0.05). Our results diverged from other pollutants in Toronto-based literature and could indicate that UFPs exhibit unique patterns of inequality. Our findings suggest a need to further study UFP dosage from an environmental inequality perspective.

Air pollution in Ontario, Canada during the COVID-19 State of Emergency

In March of 2020, the province of Ontario declared a State of Emergency (SOE) to reduce the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19). This disruption to the economy provided an opportunity to measure change in air pollution when the population spends more time at home with fewer trips. Hourly air pollution observations were obtained for fine particulate matter, nitrogen dioxide, nitrogen oxides and ozone from the Ontario air monitoring network for 2020 and the previous five years. The analysis is focused on a five-week period during the SOE with a previous five-week period used as a control. Fine particulate matter did not show any significant reductions during the SOE. Ozone concentrations at 12 of the 32 monitors were lower than any of the previous five-years; however, four locations were above average. Average ozone concentrations were 1 ppb lower during the SOE, but this ranged at individual monitors from 1.5 ppb above to 4.2 ppb below long-term conditions. Nitrogen dioxide and nitrogen oxides demonstrated a reduction across Ontario, and both pollutants displayed their lowest concentrations for 22 of 29 monitors. Individual monitors ranged from 1 ppb (nitrogen dioxide) and 5 ppb (nitrogen oxides) above average to 4.5 (nitrogen dioxide) and 7.1 ppb (nitrogen oxides) below average. Overall, both nitrogen dioxide and nitrogen oxides demonstrated a reduction across Ontario in response to the COVID-19 SOE, ozone concentrations suggested a possible reduction, and fine particulate matter has not varied from historic concentrations.

Have the Characteristics for Success as a Surgeon Changed? A Century of Perspective Through the American College of Surgeons

BACKGROUND

The Presidential Address of the American College of Surgeons (ACS) is an influential platform during the convocation for new Fellows every year. Recent work reported that most ACS presidents primarily discuss personal characteristics for success; however, these qualities were never specified. Therefore, this study aimed to identify the personal characteristics that are espoused in ACS presidential addresses as essential for success as a surgeon.

STUDY DESIGN

Thematic analysis was completed for every ACS presidential address (98 addresses between 1913 and 2019). Full-text addresses were reviewed (2 team members), personal characteristics were coded (1 team member) and then assembled into patterns and themes (3 team-members' consensus). A temporal frame was adopted in grouping these themes in that personal qualities that appeared consistently throughout this period were classified as Enduring Characteristics and those that emerged only in later years were classified as Recent Characteristics.

RESULTS

Enduring Characteristics that were present throughout the century included sincere compassion for patients; integrity; engagement (willingness to help shape the changing field at the institutional or national level); and commitment to lifelong learning. Recent Characteristics included humility and the interpersonal attributes of inclusivity and the ability to be a collaborative team leader.

CONCLUSIONS

Surgery has experienced countless paradigm shifts since 1913, and the perceived characteristics for success have similarly evolved to include more interpersonal abilities. The importance of sincere compassion for patients, integrity, engagement, and commitment to lifelong learning remained consistent for more than a century.

Risk of the Brazilian health care system over 5572 municipalities to exceed health care capacity due to the 2019 novel coronavirus (COVID-19)

The spread of the 2019 novel coronavirus (COVID-19) has challenged governments to develop public policies to reduce the load of the COVID-19 on health care systems, which is commonly referred to as "flattening the curve". This study aims to address this issue by proposing a spatial multicriteria approach to estimate the risk of the Brazilian health care system, by municipality, to exceed the health care capacity because of an influx of patients infected with the COVID-19. We estimated this risk for 5572 municipalities in Brazil using a combination of a multicriteria decision-making approach with spatial analysis to estimate the exceedance risk, and then, we examined the risk variation by designing 5 control intervention scenarios (3 scenarios representing reduction on social contacts, and 2 scenarios representing investment on health care system). For the baseline scenario using an average infection rate across Brazil, we estimated a mean Hospital Bed Capacity (HBC) value of -16.73, indicating that, on average, the Brazilian municipalities will have a deficit of approximately 17 beds. This deficit is projected to occur in 3338 municipalities with the north and northeast regions being at the greatest risk of exceeding health care capacity due to the COVID-19. The intervention scenarios indicate across all of Brazil that they could address the bed shortage, with an average of available beds between 23 and 32. However, when we consider the shortages at a municipal scale, bed exceedances still occur for at least 2119 municipalities in the most effective intervention scenario. Our findings are essential to identify priority areas, to compare populations, and to provide options for government agencies to act. This study can be used to provide support for the creation of effective health public policies for national, regional, and local intervention.

Effects of White Matter Hyperintensities on 90-Day Functional Outcome after Large Vessel and Non-Large Vessel Stroke

INTRODUCTION

White matter hyperintensity (WMH) burden is a critically important cerebrovascular phenotype related to the diagnosis and prognosis of acute ischemic stroke. The effect of WMH burden on functional outcome in large vessel occlusion (LVO) stroke has only been sparsely assessed, and direct LVO and non-LVO comparisons are currently lacking.

MATERIAL AND METHODS

We reviewed acute ischemic stroke patients admitted between 2009 and 2017 at a large healthcare system in the USA. Patients with LVO were identified and clinical characteristics, including 90-day functional outcomes, were assessed. Clinical brain MRIs obtained at the time of the stroke underwent quantification of WMH using a fully automated algorithm. The pipeline incorporated automated brain extraction, intensity normalization, and WMH segmentation.

RESULTS

A total of 1,601 acute ischemic strokes with documented 90-day mRS were identified, including 353 (22%) with LVO. Among those strokes, WMH volume was available in 1,285 (80.3%) who had a brain MRI suitable for WMH quantification. Increasing WMH volume from 0 to 4 mL, age, female gender, a number of stroke risk factors, presence of LVO, and higher NIHSS at presentation all decreased the odds for a favorable outcome. Increasing WMH above 4 mL, however, was not associated with decreasing odds of favorable outcome. While WMH volume was associated with functional outcome in non-LVO stroke (p = 0.0009), this association between WMH and functional status was not statistically significant in the complete case multivariable model of LVO stroke (p = 0.0637).

CONCLUSION

The burden of WMH has effects on 90-day functional outcome after LVO and non-LVO strokes. Particularly, increases from no measurable WMH to 4 mL of WMH correlate strongly with the outcome. Whether this relationship of increasing WMH to worse outcome is more pronounced in non-LVO than LVO strokes deserves additional investigation.

Risk Factors for Acute Ischemic Stroke Caused by Anterior Large Vessel Occlusion

Background and Purpose- Accurate prediction of acute ischemic stroke (AIS) caused by anterior large vessel occlusion (LVO) that is amendable to mechanical thrombectomy remains a challenge. We developed and validated a prediction model for anterior circulation LVO stroke using past medical history elements present on admission and neurological examination. Methods- We retrospectively reviewed AIS patients admitted between 2009 and 2017 to 3 hospitals within a large healthcare system in the United States. Patients with occlusions of the internal carotid artery or M1 or M2 segments of the middle cerebral artery were randomly split into 2/3 derivation and 1/3 validation cohorts for development of an anterior circulation LVO prediction model and score that was further curtailed for potential use in the prehospital setting. Results- A total of 1654 AIS were reviewed, including 248 (15%) with proximal anterior circulation LVO AIS. In the derivation cohort, National Institutes of Health Stroke Scale score at the time of cerebrovascular imaging, current smoking status, type 2 diabetes mellitus, extracranial carotid, and intracranial atherosclerotic stenosis was significantly associated with anterior circulation LVO stroke. The prehospital score was curtailed to National Institutes of Health Stroke Scale score, current smoking status, and type 2 diabetes mellitus. The areas under the curve for the prediction model, prehospital score, and National Institutes of Health Stroke Scale score alone were 0.796, 0.757, and 0.725 for the derivation cohort and 0.770, 0.689, and 0.665 for the validation cohort, respectively. The Youden index J was 0.46 for a score of >6 with 84.7% sensitivity and 62.0% specificity for the prediction model. Conclusions- Previously reported LVO stroke prediction scores focus solely on elements of the neurological examination. In addition to stroke severity, smoking, diabetes mellitus, extracranial carotid, and intracranial atherosclerotic stenosis were associated with anterior circulation LVO AIS. Although atherosclerotic stenosis may not be known until imaging is obtained, smoking and diabetes mellitus history can be readily obtained in the field and represent important elements of the prehospital score supplementing National Institutes of Health Stroke Scale score.

Geospatial datasets describing route geometry and ultrafine particulate matter dosage for children during shortest-distance and lowest-dosage school commutes in Toronto, Canada

The data in this article provides route geometries and ultrafine particulate dosage information for a simulation of the home-to-school walking commute for children at 296,862 residential addresses in the city of Toronto, Canada. The datasets include dosage estimates that use a modelling approach that accounts for terrain, physiology and spatial variability in ambient UFP concentrations. The dataset provides simulated routes that describe both the shortest distance route, as well as the lowest UFP dosage route. Dosage and route information are provided in both polyline (route) and point (origin address) feature classes. Included in this article is a brief description of the simulation approach taken to generate the data. For discussion and complete description of the modelling approach, please refer to “Exposure to ultrafine particulate air pollution in the school commute: Examining low-dose route optimization with terrain-enforced dosage modelling” [1].

Exposure to ultrafine particulate air pollution in the school commute: Examining low-dose route optimization with terrain-enforced dosage modelling

Exposure to ultrafine particulate air pollution (UFP) contributes to adverse health effects in sensitive population groups such as children. There is a need to explore UFP exposure in terms of respiratory dosage, which leverages the effect of activity-specific ventilation rates. Commute-related dosage, which describes the dosage that occurs during travel between fixed locations on a routine schedule (i.e. morning school commute), is often underrepresented in air pollution studies. School commutes commonly utilize active transportation modes, and modelling dosage during such commutes requires the development of an approach that captures the influence of travel mode and terrain-enforced ventilation rates. The concept of low-dosage routing is discussed as a solution to UFP dose mitigation; however, it requires an in-depth understanding of the factors that control how dosage is accumulated at different points in the commute. This paper presents a modelling workflow for examining UFP dosage while walking to school. We apply a GIS-based approach that simulates school commute routes for 296,862 homes in Toronto. We use a physical exertion-dependent dosage model that reflects broad-scale variability in physiology, travel velocity, travel gradient, and ambient UFP concentration to evaluate route-specific commute dosage. Our results reveal the patterns of within-route variation in dosage and demonstrate the effects high regional UFP concentration and accelerated physical exertion (i.e. where ventilation rate increases during uphill travel) on creating sections of greater UFP dosage within a route. We use the model to examine UFP dosage under shortest-distance and lowest-dosage routing solutions and find that 13.4% of homes had low-dosage alternative routes, while 86.6% had shortest-distances route that were already the lowest-dosage. Our findings were consistent with studies in the literature that implement a dosage modelling approach. This study highlights the importance of dosage models that account for the dynamic nature of walking speed, ventilation rate, terrain, and pollution concentration along a school commute.

Global Association of Air Pollution and Cardiorespiratory Diseases: A Systematic Review, Meta-Analysis, and Investigation of Modifier Variables

BACKGROUND

Little is known about the health risks of air pollution and cardiorespiratory diseases, globally, across regions and populations, which may differ because of external factors.

OBJECTIVES

We systematically reviewed the evidence on the association between air pollution and cardiorespiratory diseases (hospital admissions and mortality), including variability by energy, transportation, socioeconomic status, and air quality.

SEARCH METHODS

We conducted a literature search (PubMed and Web of Science) for studies published between 2006 and May 11, 2016.

SELECTION CRITERIA

We included studies if they met all of the following criteria: (1) considered at least 1 of these air pollutants: carbon monoxide, sulfur dioxide, nitrogen dioxide, ozone, or particulate matter (PM2.5 or PM10); (2) reported risk for hospital admissions, mortality, or both; (3) presented individual results for respiratory diseases, cardiovascular diseases, or both; (4) considered the age groups younger than 5 years, older than 65 years, or all ages; and (5) did not segregate the analysis by gender.

DATA COLLECTION AND ANALYSIS

We extracted data from each study, including location, health outcome, and risk estimates. We performed a meta-analysis to estimate the overall effect and to account for both within- and between-study heterogeneity. Then, we applied a model selection (least absolute shrinkage and selection operator) to assess the modifier variables, and, lastly, we performed meta-regression analyses to evaluate the modifier variables contributing to heterogeneity among studies.

MAIN RESULTS

We assessed 2183 studies, of which we selected 529 for in-depth review, and 70 articles fulfilled our study inclusion criteria. The 70 studies selected for meta-analysis encompass more than 30 million events across 28 countries. We found positive associations between cardiorespiratory diseases and different air pollutants. For example, when we considered only the association between PM2.5 and respiratory diseases ( Figure 1 , we observed a risk equal to 2.7% (95% confidence interval = 0.9%, 7.7%). Our results showed statistical significance in the test of moderators for all pollutants, suggesting that the modifier variables influence the average cardiorespiratory disease risk and may explain the varying effects of air pollution.

CONCLUSIONS

Variables related to aspects of energy, transportation, and socioeconomic status may explain the varying effect size of the association between air pollution and cardiorespiratory diseases. Public Health Implications. Our study provides a transferable model to estimate the health effects of air pollutants to support the creation of environmental health public policies for national and international intervention.

The health impacts of weekday traffic: A health risk assessment of PM2.5 emissions during congested periods

Little work has accounted for congestion, using data that reflects driving patterns, traffic volume, and speed, to examine the association between traffic emissions and human health. In this study, we performed a health risk assessment of PM_2.5 emissions during congestion periods in the Greater Toronto and Hamilton Area (GTHA), Canada. Specifically, we used a micro-level approach that combines the Stochastic User Equilibrium Traffic Assignment Algorithm with a MOVES emission model to estimate emissions considering congestion conditions. Subsequently, we applied a concentration-response function to estimate PM_2.5-related mortality, and the associated health costs. Our results suggest that traffic congestion has a substantial impact on human health and the economy in the GTHA, especially at the most congested period (7:00am). Considering daily mortality, our results showed an impact of 206 (boundary test 95%: 116; 297) and 119 (boundary test 95%: 67; 171) deaths per year (all-cause and cardiovascular mortality, respectively). The economic impact from daily mortality is approximately $1.3 billion (boundary test 95%: 0.8; 1.9), and $778 million (boundary test 95%: 478; 981), for all-cause and cardiovascular mortality, respectively. Our study can guide reliable projections of transportation and air pollution levels, improving the capability of the medical community to prepare for future trends.

Spatio-temporal analysis of particulate matter intake fractions for vehicular emissions: Hourly variation by micro-environments in the Greater Toronto and Hamilton Area, Canada

Previous investigations have reported intake fraction (iF) for different environments, which include ambient concentrations (outdoor exposure) and microenvironments (indoor exposure). However, little is known about iF variations due to space-time factors, especially in microenvironments. In this paper, we performed a spatio-temporal analysis of particulate matter (PM_2.5) intake fractions for vehicular emissions. Specifically, we investigated hourly variation (12:00am-11:00pm) by micro-environments (residences and workplaces) in the Greater Toronto and Hamilton Area (GTHA), Canada. We used GIS modeling to estimate air pollution data (ambient concentration, and traffic emission) and population data in each microenvironment. Our estimates showed that the total iF at residences and workplaces accounts for 85% and 15%, respectively. Workplaces presented the highest 24h average iF (1.06ppm), which accounted for 25% higher than residences. Observing the iF by hour at residences, our estimates showed the highest average iF at 2:00am (iF=3.72ppm). These estimates indicate that approximately 4g of PM_2.5 emitted from motor vehicles are inhaled for every million grams of PM_2.5 emitted. For the workplaces, the highest exposure was observed at 10:00am, with average iF equal to 2.04ppm. The period of the day with the lower average iF for residences was at 8:00am (average iF=0.11ppm), while for the workplaces was at 4:00am (average iF=0.47ppm). Our approach provides a new perspective on human exposure to air pollution. Our results showed significant hourly variation in iF across the GTHA. Our findings can be incorporated in future investigations to advance environmental health effects research and human health risk assessment.

Association of PM2.5 with diabetes, asthma, and high blood pressure incidence in Canada: A spatiotemporal analysis of the impacts of the energy generation and fuel sales

Numerous studies have reported an association between fine particulate matter (PM_2.5) and human health. Often these relationships are influenced by environmental factor that varies spatially and/or temporally. To our knowledge, there are no studies in Canada that have considered energy generation and fuel sales as PM_2.5 effects modifiers. Determining exposure and disease-specific risk factors over space and time is crucial for disease prevention and control. In this study, we evaluated the association of PM_2.5 with diabetes, asthma, and High Blood Pressure (HBP) incidence in Canada. Then we explored the impact of the energy generation and fuel sales on association changes. We fit an age-period-cohort as the study design, and we applied an over-dispersed Poisson regression model to estimate the risk. We conducted a sensitivity analysis to explore the impact of variation in clean energy rates and fuel sales on outcomes changes. The study included 117 health regions in Canada between 2007 and 2014. Our findings showed strong association of PM_2.5 with diabetes, asthma, and HBP incidence. A two-year increase of 10μg/m³ in PM_2.5 was associated with an increased risk of 5.34% (95% CI: 2.28%; 12.53%) in diabetes incidence, 2.24% (95% CI: 0.93%; 5.38%) in asthma incidence, and 8.29% (95% CI: 3.44%; 19.98%) in HBP incidence. Our sensitivity analysis findings suggest higher risks of diabetes, asthma and HBP incidence when there is low clean energy generation. On the other hand, we found lower risk when we considered high rate of clean energy generation. For example, considering only diabetes incidence, we found that the risk in health regions with low rates of clean electricity is approximately 700% higher than the risk in health regions with high rates of clean electricity. Furthermore, our analysis suggested that the risk in regions with low fuel sales is 66% lower than the risk is health regions with low rates of clean electricity. Our study provides support for the creation of effective environmental health public policies that take into account the risk factors present in Canadians health regions.

Spatiotemporal analysis of traffic emissions in over 5000 municipal districts in Brazil

Exposure to traffic emission is harmful to human health. Emission inventories are essential to public health policies aiming at protecting human health, especially in areas with incomplete or nonexistent air pollution monitoring networks. In Brazil, for example, only 1.7% of municipal districts have a monitoring network, and only a few studies have reported data on vehicle emission inventories. No studies have presented emission inventories by municipality. In this study, we predicted vehicular emissions for 5570 municipal districts in Brazil during the period 2001-2012. We used a top-down method to estimate emissions. Carbon dioxide (CO₂) is the pollutant with the highest emissions, with approximately 190 million tons per year during the period 2001-2012). For the other traffic-related pollutants, we predicted annual emissions of 1.5 million tons for carbon monoxide (CO), 1.2 million tons of nitrogen oxides (NO_x), 209,000 tons of nonmethane hydrocarbons (NMHC), 58,000 tons of particulate matter (PM), and 42,000 tons for methane (CH₄). From 2001 to 2012, CO, NMHC, and PM emissions decreased by 41, 33, and 47%, respectively, whereas those CH₄, NO_x, and CO₂ increased by 2, 4, and 84%, respectively. We estimated uncertainties in our study and found that NO_x was the pollutant with the lowest percentage difference, 8%, and NMHC with the highest one, 30%. For CO, CH₄, CO₂, and PM, the values were 22, 14, 21, and 20%, respectively. Finally, we found that during 2001 and 2012 emissions increased in the Northwest and Northeast. In contrast, pollutant emissions, except for CO₂, decreased in the Southeast, South, and part of Midwest. Our predictions can be critical to efforts developing cost-effective public policies tailored to individual municipal districts in Brazil.

IMPLICATIONS

Emission inventories may be an alternative approach to provide data for air quality forecasting in areas where air quality data are not available. This approach can be an effective tool in developing spatially resolved emission inventories.

Mapping distance-decay of cardiorespiratory disease risk related to neighborhood environments

Neighborhood characteristics affect an individual's quality of life. Although several studies have examined the relationship between neighborhood environments and human health, we are unaware of studies that have examined the distance-decay of this effect and then presented the risk results spatially. Our study is unique in that is explores the health effects in a less developed country compared to most studies that have focused on developed countries. The objective of our study is to quantify the distance-decay cardiorespiratory diseases risk related to 28 neighborhood aspects in the Federal District, Brazil and present this information spatially through risk maps of the region. Toward this end, we used a quantile regression model to estimate risk and GIS modeling techniques to create risk maps. Our analysis produced the following findings: i) a 2500 m increase in highway length was associated with a 46% increase in cardiorespiratory diseases; ii) 46,000 light vehicles in circulation (considering a buffer of ≤500 m from residences) was associated with 6 hospital admissions (95% CI: 2.6, 14.6) per cardiorespiratory diseases; iii) 74,000 m² of commercial areas (buffer ≤1700 m) was associated with 12 hospital admissions (95% CI: 2.2, 20.8); iv) 1km² increase in green areas intra urban was associated with less two hospital admissions, and; vi) those who live ≤500 m from the nearest point of wildfire are more likely to have cardiorespiratory diseases that those living >500 m. Our findings suggest that the approach used in this study can be an option to improve the public health policies.

Association between vehicular emissions and cardiorespiratory disease risk in Brazil and its variation by spatial clustering of socio-economic factors

Many studies have suggested that socio-economic factors are strong modifiers of human vulnerability to air pollution effects. Most of these studies were performed in developed countries, specifically in the US and Europe. Only a few studies have been performed in developing countries, and analyzed small regions (city level) with no spatial disaggregation. The aim of this study was to assess the association between vehicle emissions and cardiorespiratory disease risk in Brazil and its modification by spatial clustering of socio-economic conditions. We used a quantile regression model to estimate the risk and a geostatistical approach (K means) to execute spatial cluster analysis. We performed the risk analysis in three stages. First, we analyzed the entire study area (primary analysis), and then we conducted a spatial cluster analysis based on various municipal-level socio-economic factors, followed by a sensitivity analysis. We studied 5444 municipalities in Brazil between 2008 and 2012. Our findings showed a significant association between cardiorespiratory disease risk and vehicular emissions. We found that a 15% increase in air pollution is associated with a 6% increase in hospital admissions rates. The results from the spatial cluster analysis revealed two groups of municipalities with distinct sets of socio-economic factors and risk levels of cardiorespiratory disease related to exposure to vehicular emissions. For example, for vehicle emissions of PM in 2008, we found a relative risk of 4.18 (95% CI: 3.66, 4.93) in the primary analysis; in Group 1, the risk was 0.98 (95% CI: 0.10, 2.05) while in Group 2, the risk was 5.56 (95% CI: 4.46, 6.25). The risk in Group 2 was 480% higher than the risk in Group 1, and 35% higher than the risk in the primary analysis. Group 1 had higher values (3rd quartile) for urbanization rate, highway density, and GDP; very high values (≥3rd quartile) for population density; median values for distance from the capital; and lower values (1st quartile) for rural population density. Group 2 had lower values (1st quartile) urbanization rate; median values for highway density, GDP, and population density; between median and third quartile values for distance from the capital; and higher values (3rd quartile) for rural population density. Our findings suggest that socio-economic factors are important modifiers of the human risk of cardiorespiratory disease due to exposure to vehicle emissions in Brazil. Our study provides support for creating effective public policies related to environmental health that are targeted to high-risk populations.

Mapping real-time air pollution health risk for environmental management: Combining mobile and stationary air pollution monitoring with neural network models

Air pollution poses health concerns at the global scale. The challenge of managing air pollution is significant because of the many air pollutants, insufficient funds for monitoring and abatement programs, and political and social challenges in defining policy to limit emissions. Some governments provide citizens with air pollution health risk information to allow them to limit their exposure. However, many regions still have insufficient air pollution monitoring networks to provide real-time mapping. Where available, these risk mapping systems either provide absolute concentration data or the concentrations are used to derive an Air Quality Index, which provides the air pollution risk for a mix of air pollutants with a single value. When risk information is presented as a single value for an entire region it does not inform on the spatial variation within the region. Without an understanding of the local variation residents can only make a partially informed decision when choosing daily activities. The single value is typically provided because of a limited number of active monitoring units in the area. In our work, we overcome this issue by leveraging mobile air pollution monitoring techniques, meteorological information and land use information to map real-time air pollution health risks. We propose an approach that can provide improved health risk information to the public by applying neural network models within a framework that is inspired by land use regression. Mobile air pollution monitoring campaigns were conducted across Hamilton from 2005 to 2013. These mobile air pollution data were modelled with a number of predictor variables that included information on the surrounding land use characteristics, the meteorological conditions, air pollution concentrations from fixed location monitors, and traffic information during the time of collection. Fine particulate matter and nitrogen dioxide were both modelled. During the model fitting process we reserved twenty percent of the data to validate the predictions. The models' performances were measured with a coefficient of determination at 0.78 and 0.34 for PM2.5 and NO2, respectively. We apply a relative importance measure to identify the importance of each variable in the neural network to partially overcome the black box issues of neural network models.

Longitudinal myelitis, aseptic meningitis, and conus medullaris infarction as presenting manifestations of pediatric sysemic lupus erythematosus

A healthy boy developed subacutely progressive quadriparesis, complicated by sudden paraplegia, fever, and meningeal signs, diagnosed as longitudinal myelitis, aseptic meningitis, and conus medullaris infarction and identified as the presenting manifestations of neuropsychiatric systemic lupus erythematosus. Rapid expansion of the conus on serial neuroimaging led to emergent decompressive laminectomy and cord biopsy showing vasculitis and cord infarction. The patient had partial recovery after treatment with high-dose steroids. Increased vigilance is required when pediatric patients develop a similar subacute presentation on the ground of active systemic lupus erythematosus because it may herald the onset of a catastrophic neurological syndrome.

Sequencing the genome of Plasmodium falciparum

Advances in microbial genomic sequencing have the potential to revolutionize the control of infectious diseases. Recently, a consortium of researchers and funding agencies from the United States and Great Britain have embarked on a project to sequence the genome from Plasmodium falciparum, the most important cause of human malaria. The Malaria Genome Sequencing Project has reached an important milestone with the completion of the entire DNA sequence and annotation of chromosome 2, a 950 kilobase chromosome of Plasmodium falciparum. This review article will provide an overview of the malaria genome sequencing project, highlight progress in the field of microbial sequencing, and suggest new directions for future malaria research.

The Malaria Genome Sequencing Project

An international consortium of genome centres, advanced development teams and funding agencies has begun the task of sequencing the genome of the parasite Plasmodium falciparum, the most important cause of human malaria. Sequencing is proceeding chromosome by chromosome, and the annotated sequence of chromosome 2 is nearly finished. With the continual release of sequence data as they are generated, malaria researchers have access to a steady stream of genomic sequences and will soon have the complete annotation of all of the estimated 5000-7000 P. falciparum genes. The task will then be how to best apply these data to the development of new anti-malarial drugs, vaccines and diagnostic tests. This review provides a brief overview of the Malaria Genome Sequencing Project and suggests potential directions for future malaria research.

Implications of the human genome for understanding human biology and medicine

Clinical researchers, practicing physicians, patients, and the general public now live in a world in which the 2.9 billion nucleotide codes of the human genome are available as a resource for scientific discovery. Some of the findings from the sequencing of the human genome were expected, confirming knowledge presaged by many decades of research in both human and comparative genetics. Other findings are unexpected in their scientific and philosophical implications. In either case, the availability of the human genome is likely to have significant implications, first for clinical research and then for the practice of medicine. This article provides our reflections on what the new genomic knowledge might mean for the future of medicine and how the new knowledge relates to what we knew in the era before the availability of the genome sequence. In addition, practicing physicians in many communities are traditionally also ambassadors of science, called on to translate arcane data or the complex ramifications of biology into a language understood by the public at large. This article also may be useful for physicians who serve in this capacity in their communities. We address the following issues: the number of protein-coding genes in the human genome and certain classes of noncoding repeat elements in the genome; features of genome evolution, including large-scale duplications; an overview of the predicted protein set to highlight prominent differences between the human genome and other sequenced eukaryotic genomes; and DNA variation in the human genome. In addition, we show how this information lays the foundations for ongoing and future endeavors that will revolutionize biomedical research and our understanding of human health.

An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element

P element somatic inhibitor (PSI) is a 97-kDa RNA-binding protein with four KH motifs that is involved in the inhibition of splicing of the Drosophila P element third intron (IVS3) in somatic cells. PSI interacts with a negative regulatory element in the IVS3 5' exon. This element contains two pseudo-5' splice sites, termed F1 and F2. To identify high affinity binding sites for the PSI protein, in vitro selection (SELEX) was performed using a random RNA oligonucleotide pool. Alignment of high affinity PSI-binding RNAs revealed a degenerate consensus sequence consisting of a short core motif of CUU flanked by alternative purines and pyrimidines. Interestingly, this sequence resembles the F2 pseudo-5' splice site in the P element negative regulatory element. Additionally, a negative in vitro selection of PCR-mutagenized P element 5' exon regulatory element RNAs identified two U residues in the F1 and F2 pseudo-5' splice sites as important nucleotides for PSI binding and the U residue in the F2 region is a nearly invariant nucleotide in the consensus SELEX motif. The high affinity PSI SELEX sequence acted as a splicing inhibitor when placed in the context of a P element splicing pre-mRNA in vitro. Data from in vitro splicing assays, UV crosslinking and RNA-binding competition experiments indicates a strong correlation between the binding affinities of PSI for the SELEX sequences and their ability to modulate splicing of P element IVS3 in vitro.

Modulation of P-element pre-mRNA splicing by a direct interaction between PSI and U1 snRNP 70K protein

P-element somatic inhibitor (PSI) is a KH domain-containing splicing factor highly expressed in Drosophila somatic tissues. Here we have identified a direct association of PSI with the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) particle in somatic nuclear extracts. This interaction is mediated by highly conserved residues within the PSI C-terminal AB motif and the U1 snRNP-specific 70K protein. Through the AB motif, PSI modulates U1 snRNP binding on the P-element third intron (IVS3) 5' splice site and its upstream exonic regulatory element. Ectopic expression experiments in the Drosophila female germline demonstrate that the AB motif also contributes to IVS3 splicing inhibition in vivo. These data show that the processing of specific target transcripts, such as the P-element mRNA, is regulated by a functional PSI-U1 snRNP interaction in Drosophila.

Toxicological assessment of gadoversetamide injection (OptiMARK), a new contrast-enhancement agent for use in magnetic resonance imaging

RATIONALE AND OBJECTIVES

A series of preclinical tests were undertaken during the developmental process to determine the safety profile of gadoversetamide injection (OptiMARK).

METHODS

Acute intravenous, acute intracisternal, and repeated-dose toxicities; cardiovascular effects; and genetic and reproductive toxicology characteristics were assessed in several animal species.

RESULTS

Gadoversetamide injection demonstrated an acute intravenous median lethal dose of 25 to 28 mmol/kg and a maximum nonlethal dose of 14 mmol/kg in mice. In the dog, acute administration of gadoversetamide injection showed a no observable effect level at 3 mmol/kg. Dosed daily for 4 weeks, gadoversetamide injection (0.1 mmol x kg(-1) x d(-1)) caused no serious irreversible changes in any organs in rats and dogs. At a dose of 0.1 mmol/kg, gadoversetamide injection caused no significant (P < 0.05) changes in cardiovascular function in anesthetized dogs. Gadoversetamide injection showed no mutagenic activity. Fertility, reproductive performance, and postnatal fetal development were not affected at doses up to 0.5 mmol x kg(-1) x d(-1) in the rat. No teratogenicity was observed at doses up to 4.2 mmol x kg(-1) x d(-1) in the rat and up to 1.6 mmol x kg(-1) x d(-1) in the rabbit.

CONCLUSIONS

Data from our toxicological assessment demonstrate the safety of gadoversetamide injection in a number of animal species at doses exceeding the intended human clinical dose.

Mutation screening of the TNFRSF11A gene encoding receptor activator of NF kappa B (RANK) in familial and sporadic Paget's disease of bone and osteosarcoma

Paget's disease of bone (PDB) is a common disorder characterized by focal areas of increased and disorganized osteoclastic bone resorption, leading to bone pain, deformity, pathological fracture, and an increased risk of osteosarcoma. Genetic factors play an important role in the pathogenesis of Paget's disease. In some families, the disease has been found to be linked to a susceptibility locus on chromosome 18q21-22, which also contains the gene responsible for familial expansile osteolysis (FEO)--a rare bone dysplasia with many similarities to Paget's disease. Insertion mutations of the TNFRSF11A gene encoding Receptor Activator of NF kappa B (RANK) have recently been found to be responsible for FEO and rare cases of early onset familial Paget's disease. Loss of heterozygosity (LOH) affecting the PDB/FEO critical region has also been described in osteosarcomas suggesting that TNFRSF11A might also be involved in the development of osteosarcoma. In order to investigate the possible role of TNFRSF11A in the pathogenesis of Paget's disease and osteosarcoma, we conducted mutation screening of the TNFRSF11A gene in patients with familial and sporadic Paget's disease as well as DNA extracted from Pagetic bone lesions, an osteosarcoma arising in Pagetic bone and six osteosarcoma cell lines. No specific abnormalities of the TNFRSF11A gene were identified in a Pagetic osteosarcoma, the osteosarcoma cell lines, DNA extracted from Pagetic bone lesions, or DNA extracted from peripheral blood in patients with familial or sporadic Paget's disease including several individuals with early onset Paget's disease. These data indicate that TNFRSF11A mutations contribute neither to the vast majority of cases of sporadic or familial PDB, nor to the development of osteosarcoma.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

MRI contrast enhancement of necrosis by MP-2269 and gadophrin-2 in a rat model of liver infarction

RATIONALE AND OBJECTIVES

The mechanisms of action leading to specific localization of necrosis-avid contrast agents (NACAs) such as gadophrin-2 are not well defined. It has been suggested recently that agents with a high degree of serum albumin binding may also serve as NACAs by virtue of nonspecific hydrophobic interactions. The present MRI-histomorphology correlation study was conducted to verify the likelihood of the proposed albumin-binding mechanism by comparing an albumin-binding blood pool agent, MP-2269, with gadophrin-2 in a rat model of reperfused liver infarction.

METHODS

Reperfused infarction in the right liver lobe was surgically induced in six rats. Serial T1-weighted MRI was performed before and after intravenous injection of MP-2269 at 0.05 mmol/kg and repeated in the same rats 24 hours later after intravenous injection of gadophrin-2 at the same dosage (0.05 mmol/kg). The MR images were matched with corresponding histomorphological findings. The signal intensity and contrast ratio of infarcted and normal hepatic lobes were quantified and compared between the two agents during the postcontrast course.

RESULTS

Before contrast, the infarcted lobe was indiscernible from normal liver on T1-weighted MRI. Shortly after injection of both MP-2269 and gadophrin-2, a negative contrast occurred between infarcted and normal liver because of a strong liver signal intensity enhancement and an inferior uptake in the necrotic liver. On delayed phase (>60 minutes), a necrosis-specific contrast enhancement (contrast ratio 1.6) developed with gadophrin-2 but not with MP-2269. The MR images matched well with corresponding histomorphological findings.

CONCLUSIONS

Although both MP-2269 and gadophrin-2 feature an albumin-binding capacity, only gadophrin-2 displayed a persistent necrosis-specific contrast enhancement in the rat model of reperfused liver infarction. Therefore, the role of albumin binding in the mechanisms of NACAs should be reevaluated.

A 500-kb region on chromosome 16p13.1 contains the pseudoxanthoma elasticum locus: high-resolution mapping and genomic structure

We have recently mapped the genetic defect underlying pseudoxanthoma elasticum (PXE), an inherited disorder characterized by progressive calcification of elastic fibers in skin, eye, and cardiovascular system, to chromosome 16p 13.1. Here we report further data on the fine-mapping and genomic structure of this locus. Haplotype analysis of informative PXE families narrowed the locus to an interval of less than 500 kb located between markers D16B9621 and D16S764. Three overlapping YAC clones were found to cover this region through YAC-STS content mapping. An overlapping BAC contig was then constructed to cover this interval and the surrounding region. About 80% of this chromosomal region has been fully sequenced using the BAC shotgun technique. Gene content and sequence analysis predicted four genes (MRP1, MRP6, PM5, and a novel transcript) and two pseudogenes (ARA and PKDI) within this interval. By screening a somatic cell hybrid panel we were able to precision-map the breakpoint of Cy185 and the starting point of a chromosomal duplication within 20 kb of BAC A962B4. The present data further refine the localization of PXE, provide additional physical cloning resources, and will aid in the eventual identification of the genetic defect causing PXE.

The genome sequence of Drosophila melanogaster

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

A whole-genome assembly of Drosophila

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

Human BAC ends quality assessment and sequence analyses

End sequences from bacterial artificial chromosomes (BACs) provide highly specific sequence markers in large-scale sequencing projects. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length of >460 bp for a total of 141 Mb covering approximately 4.7% of the genome. Over 60% of the clones have BAC end sequences (BESs) from both ends representing more than fivefold coverage of the human genome by the paired-end clones. Our quality assessments and sequence analyses indicate that BESs from human BAC libraries developed at The California Institute of Technology (CalTech) and Roswell Park Cancer Institute have similar properties. The analyses have highlighted differences in insert size for different segments of the CalTech library. Problems with the fidelity of tracking of sequence data back to physical clones have been observed in some subsets of the overall BES dataset. The annotation results of BESs for the contents of available genomic sequences, sequence tagged sites, expressed sequence tags, protein encoding regions, and repeats indicate that this resource will be valuable in many areas of genome research.

Reversible integer-to-integer wavelet transforms for image compression: performance evaluation and analysis

In the context of image coding, a number of reversible integer-to-integer wavelet transforms are compared on the basis of their lossy compression performance, lossless compression performance, and computational complexity. Of the transforms considered, several were found to perform particularly well, with the best choice for a given application depending on the relative importance of the preceding criteria. Reversible integer-to-integer versions of numerous transforms are also compared to their conventional (i.e., nonreversible real-to-real) counterparts for lossy compression. At low bit rates, reversible integer-to-integer and conventional versions of transforms were found to often yield results of comparable quality. Factors affecting the compression performance of reversible integer-to-integer wavelet transforms are also presented, supported by both experimental data and theoretical arguments.

Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11

We have determined the detailed molecular structure and evolution of an alpha satellite junction from human chromosome 16p11. The analysis reveals that the alpha satellite sequence bordering the transition lacks higher-order structure and that the non-alpha satellite portion consists of a mosaic of duplicated segments of complex evolutionary origin. The 16p11 junction was formed recently (5-10 million years ago) by the duplication and transposition of genomic segments from Xq28 and 4q24. Once this mosaic structure was formed, a larger complex was spread among multiple pericentromeric regions. This resulted in the formation of large (>62 kb) paralogous segments that share a high degree ( approximately 97%) of sequence similarity. Both phylogenetic and comparative analyses indicate that these pericentromeric-directed duplications occurred around the time of the divergence of the human, gorilla and chimpanzee lineages, resulting in the subtle restructuring of the primate genome among these species. The available data suggest that such chimeric structures are a general property of several different human chromosomes near their alpha satellite junctions.

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.

Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q

Several publicly funded large-scale sequencing efforts have been initiated with the goal of completing the first reference human genome sequence by the year 2005. Here we present the results of analysis of 11.8 Mb of genomic sequence from chromosome 16. The apparent gene density varies throughout the region, but the number of genes predicted (84) suggests that this is a gene-poor region. This result may also suggest that the total number of human genes is likely to be at the lower end of published estimates. One of the most interesting aspects of this region of the genome is the presence of highly homologous, recently duplicated tracts of sequence distributed throughout the p-arm. Such duplications have implications for mapping and gene analysis as well as the predisposition to recurrent chromosomal structural rearrangements associated with genetic disease.

Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome

The sequence-tagged connector (STC) strategy proposes to generate sequence tags densely scattered (every 3.3 kilobases) across the human genome by arraying 450,000 bacterial artificial chromosomes (BACs) with randomly cleaved inserts, sequencing both ends of each, and preparing a restriction enzyme fingerprint of each. The STC resource, containing end sequences, fingerprints, and arrayed BACs, creates a map where the interrelationships of the individual BAC clones are resolved through their STCs as overlapping BAC clones are sequenced. Once a seed or initiation BAC clone is sequenced, the minimum overlapping 5' and 3' BAC clones can be identified computationally and sequenced. By reiterating this "sequence-then-map by computer analysis against the STC database" strategy, a minimum tiling path of clones can be sequenced at a rate that is primarily limited by the sequencing throughput of individual genome centers. As of February 1999, we had deposited, together with The Institute for Genomic Research (TIGR), into GenBank 314,000 STCs ( approximately 135 megabases), or 4.5% of human genomic DNA. This genome survey reveals numerous genes, genome-wide repeats, simple sequence repeats (potential genetic markers), and CpG islands (potential gene initiation sites). It also illustrates the power of the STC strategy for creating minimum tiling paths of BAC clones for large-scale genomic sequencing. Because the STC resource permits the easy integration of genetic, physical, gene, and sequence maps for chromosomes, it will be a powerful tool for the initial analysis of the human genome and other complex genomes.

1H-NMRD and 17O-NMR assessment of water exchange and rotational dynamics of two potential MRI agents: MP-1177 (an extracellular agent) and MP-2269 (a blood pool agent)

The parameters that govern water proton magnetic relaxation (e.g. water exchange rates, and rotational and electronic correlation times) of representatives of two classes of Gd(III) complexes have been estimated, using two different approaches and the results compared with those derived for known analogs. The complexes studied are: (i) the non-ionic GdDTPA-bis(-methoxyethyl-amide) [Gd(DTPA-BMEA)], a typical small-molecule extracellular MR agent, and (ii) the ionic Gd(III) complex of 4-pentylbicyclo[2.2.2]octane-1-carboxyl-di-L-aspartyl-lysine-deriv ed-DTPA [GdL]4-, a prototype MR blood pool agent, which binds to serum albumin in vivo through non-covalent hydrophobic interactions. An 17O-NMR study of [Gd(DTPA-BMEA)] gives a water exchange rate constant of k(ex)298 = (0.39 +/- 0.02) x 10(6) s(-1), identical to that for the bismethylamide analog [Gd(DTPA-BMA)]. Both approaches yield longer rotational correlation times for [Gd(DTPA-BMEA)], consistent with its higher molecular weight. An 17O-NMR study of [GdL]4- gives a water exchange rate constant of k(ex)298 = (4.2 +/- 0.1) x 10(6) s(-1), identical to that for [Gd(DTPA)]2-. The water exchange rate on [GdL]4- did not decrease considerably when bound to albumin, the lowest limit is k(ex,GdL-BSA) = k(ex,GdL)/2. Both approaches yield identical rotational correlation times for [GdL]4-, however, it was difficult to derive a consistent rotational constant for the albumin-bound [GdL]4- using the different approaches (values ranged between 1.0 and 23.0 ns).

A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2

We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1-p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which-corresponding to a total of 7.721 Mb of genomic DNA-have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is approximately 3.5 x deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs.

High throughput direct end sequencing of BAC clones

Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large genomic regions. For this strategy to be effective, high throughput methods for BAC end sequencing of all the clones in deep coverage BAC libraries needed to be developed. Here we describe a low cost, efficient, 96 well procedure for BAC end sequencing. These methods allow us to generate BAC end sequences from human and Arabidoposis libraries with an average read length of >450 bases and with a single pass sequencing average accuracy of >98%. Application of BAC end sequences in genomic sequen-cing is discussed.