Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data.

Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA expression profiles from a single sequencing library. Cytotoxicity due to extended periods of labelling or high 4sU concentrations has been described, but the effects of extensive 4sU labelling on expression estimates from nucleotide conversion RNA-seq have not been studied. Here, we performed nucleotide conversion RNA-seq with escalating doses of 4sU with short-term labelling (1h) and over a progressive time course (up to 2h) in different cell lines. With high concentrations or at later time points, expression estimates were biased in an RNA half-life dependent manner. We show that bias arose by a combination of reduced mappability of reads carrying multiple conversions, and a global, unspecific underrepresentation of labelled RNA emerging during library preparation and potentially global reduction of RNA synthesis. We developed a computational tool to rescue unmappable reads, which performed favourably compared to previous read mappers, and a statistical method, which could fully remove remaining bias. All methods developed here are freely available as part of our GRAND-SLAM pipeline and grandR package.

Multimodal Surveillance Model for Enterovirus D68 Respiratory Disease and Acute Flaccid Myelitis among Children in Colorado, USA, 2022.

Surveillance for emerging pathogens is critical for developing early warning systems to guide preparedness efforts for future outbreaks of associated disease. To better define the epidemiology and burden of associated respiratory disease and acute flaccid myelitis (AFM), as well as to provide actionable data for public health interventions, we developed a multimodal surveillance program in Colorado, USA, for enterovirus D68 (EV-D68). Timely local, state, and national public health outreach was possible because prospective syndromic surveillance for AFM and asthma-like respiratory illness, prospective clinical laboratory surveillance for EV-D68 among children hospitalized with respiratory illness, and retrospective wastewater surveillance led to early detection of the 2022 outbreak of EV-D68 among Colorado children. The lessons learned from developing the individual layers of this multimodal surveillance program and how they complemented and informed the other layers of surveillance for EV-D68 and AFM could be applied to other emerging pathogens and their associated diseases.

Cerebellar Volume and Disease Staging in Parkinson's Disease: An ENIGMA-PD Study.

BACKGROUND: Increasing evidence points to a pathophysiological role for the cerebellum in Parkinson's disease (PD). However, regional cerebellar changes associated with motor and non-motor functioning remain to be elucidated. OBJECTIVE: To quantify cross-sectional regional cerebellar lobule volumes using three dimensional T1-weighted anatomical brain magnetic resonance imaging from the global ENIGMA-PD working group. METHODS: Cerebellar parcellation was performed using a deep learning-based approach from 2487 people with PD and 1212 age and sex-matched controls across 22 sites. Linear mixed effects models compared total and regional cerebellar volume in people with PD at each Hoehn and Yahr (HY) disease stage, to an age- and sex- matched control group. Associations with motor symptom severity and Montreal Cognitive Assessment scores were investigated. RESULTS: Overall, people with PD had a regionally smaller posterior lobe (dmax = -0.15). HY stage-specific analyses revealed a larger anterior lobule V bilaterally (dmax = 0.28) in people with PD in HY stage 1 compared to controls. In contrast, smaller bilateral lobule VII volume in the posterior lobe was observed in HY stages 3, 4, and 5 (dmax = -0.76), which was incrementally lower with higher disease stage. Within PD, cognitively impaired individuals had lower total cerebellar volume compared to cognitively normal individuals (d = -0.17). CONCLUSIONS: We provide evidence of a dissociation between anterior "motor" lobe and posterior "non-motor" lobe cerebellar regions in PD. Whereas less severe stages of the disease are associated with larger motor lobe regions, more severe stages of the disease are marked by smaller non-motor regions. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

The role of laboratory investigations in the classification of tremors.

INTRODUCTION: Tremor is the most common movement disorder. Although clinical examination plays a significant role in evaluating patients with tremor, laboratory tests are useful to classify tremors according to the recent two-axis approach proposed by the International Parkinson and Movement Disorders Society. METHODS: In the present review, we will discuss the usefulness and applicability of the various diagnostic methods in classifying and diagnosing tremors. We will evaluate a number of techniques, including laboratory and genetic tests, neurophysiology, and neuroimaging. The role of newly introduced innovative tremor assessment methods will also be discussed. RESULTS: Neurophysiology plays a crucial role in tremor definition and classification, and it can be useful for the identification of specific tremor syndromes. Laboratory and genetic tests and neuroimaging may be of paramount importance in identifying specific etiologies. Highly promising innovative technologies are being developed for both clinical and research purposes. CONCLUSIONS: Overall, laboratory investigations may support clinicians in the diagnostic process of tremor. Also, combining data from different techniques can help improve understanding of the pathophysiological bases underlying tremors and guide therapeutic management.

Strain-Correlated Piezoelectricity in Quasi-Two-Dimensional Zinc Oxide Nanosheets.

Two-dimensional (2D) piezoelectric materials have recently drawn intense interest in studying the nanoscale electromechanical coupling phenomenon and device development. A critical knowledge gap exists to correlate the nanoscale piezoelectric property with the static strains often found in 2D materials. Here, we present a study of the out-of-plane piezoelectric property of nanometer-thick 2D ZnO-nanosheets (NS) in correlation to in-plane strains, using in situ via strain-correlated piezoresponse force microscopy (PFM). We show that the strain configuration (either tensile or compressive) can dramatically influence the measured piezoelectric coefficient (d33) of 2D ZnO-NS. A comparison of the out-of-plane piezoresponse is made for in-plane tensile and compressive strains approaching 0.50%, where the measured d33 varies between 2.1 and 20.3 pm V-1 resulting in an order-of-magnitude change in the piezoelectric property. These results highlight the important role of in-plane strain in the quantification and application of 2D piezoelectric materials.

Detecting New Sources of Childhood Environmental Lead Exposure Using a Statistical Surveillance System, 2015-2019.

Objectives. To design and implement a statistical surveillance system to prospectively identify potential clusters of elevated blood lead levels (EBLLs) in children younger than 6 years in the Denver, Colorado, metro area. Methods. We evaluated the ability of 2 independent statistical surveillance methods to detect synthetic clusters of EBLLs in Denver between 2015 and 2019. Results. Together, the statistical surveillance methods took an average of 9 months to detect the synthetic clusters. This is faster than similar real-world clusters that have been reported in the past. The system was relatively unaffected by changes in the testing rate and to the blood lead reference value. Conclusions. The adequate design of a statistical surveillance system can help increase the rate at which clusters of EBLLs are detected in Denver, but doing so requires an accurate model of the spatial distribution of EBLLs. Earlier detection of clusters can help guide more effective public health interventions at the local level. (Am J Public Health. 2022;112(S7):S715-S722. https://doi.org/10.2105/AJPH.2022.307009).

Developmental trauma: Conceptual framework, associated risks and comorbidities, and evaluation and treatment.

Children exposed to adverse childhood experiences (ACEs) and pervasive interpersonal traumas may go on to develop PTSD and, in most cases, will further undergo a significant shift in their developmental trajectory. This paper examines contemporary research on Developmental Trauma (DT), which is inextricably linked to disruptions in social cognition, physiological and behavioral regulation, and parent-child attachments. Developmental trauma associated with early experiences of abuse or neglect leads to multi-faceted and longstanding consequences and underscores critical periods of development, complex stress-mediated adaptations, and multilevel, trans-theoretical influences in the diagnostic formulation and treatment of traumatized children, adolescents, and adults. Psychological and medical correlates of Developmental Trauma Disorder are considered, and directions for future research are discussed.

The Role of the Cerebellum in Tremor - Evidence from Neuroimaging.

Background: Neuroimaging research has played a key role in identifying which cerebral changes are associated with tremor. Here we will focus on the cerebellum, which may drive tremor oscillations, process tremor-related afferents, modulate activity in remote brain regions, or a combination. Methods: On the 6th of October 2021, we conducted a PubMed search to select articles providing neuroimaging evidence for cerebellar involvement in essential tremor (ET), Parkinson's disease (PD) tremor, and dystonic tremor (DT). Results: In ET, tremor-related activity is found in motor areas of the bilateral cerebellum, and altered functional connectivity within and outside the cerebellum correlates with tremor severity. Furthermore, ET is associated with cerebellar atrophy, but also with compensatory structural changes outside the cerebellum (e.g. supplementary motor area). In PD, tremor-related cerebellar activity and increased cerebello-thalamic coupling has been found. Emerging evidence suggests that the cerebellum plays a key role in dopamine-resistant rest tremor and in postural tremor. Cerebellar structural alterations have been identified in PD, but only some relate to tremor. DT is associated with more widespread cerebral networks than other tremor types. Discussion: In ET, the cerebellum likely acts as an oscillator, potentially due to loss of inhibitory mechanisms. In contrast, in PD the cerebellum may be a modulator, which contributes to tremor oscillations by influencing the thalamo-cortical system. The precise role of the cerebellum in DT remains unclear. We recommend that future research measures tremor-related activity directly by combining electrophysiology with neuroimaging, while brain stimulation techniques may be used to establish causality. Highlights: This review of neuroimaging studies has provided convincing evidence that the cerebellum plays a key role in the pathophysiology of ET, PD tremor, and dystonic tremor syndromes. This contribution may consist of driving tremor oscillations, processing tremor-related afferents, modulating activity in remote brain regions, or all the above.

Long-term air pollution and other risk factors associated with COVID-19 at the census tract level in Colorado.

Previous nationwide studies have reported links between long-term concentrations of fine particulate matter (PM2.5) and COVID-19 infection and mortality rates. In order to translate these results to the state level, we use Bayesian hierarchical models to explore potential links between long-term PM2.5 concentrations and census tract-level rates of COVID-19 outcomes (infections, hospitalizations, and deaths) in Colorado. We explicitly consider how the uncertainty in PM2.5 estimates affects our results by comparing four different PM2.5 surfaces from academic and governmental organizations. After controlling for 20 census tract-level covariates, we find that our results depend heavily on the choice of PM2.5 surface. Using PM2.5 estimates from the United States EPA, we find that a 1 µg/m3 increase in long-term PM2.5 concentrations is associated with a statistically significant 26% increase in the relative risk of hospitalizations and a 34% increase in mortality. Results for all other surfaces and outcomes were not statistically significant. At the same time, we find a clear association between communities of color and COVID-19 outcomes at the Colorado census tract level that is minimally affected by the choice of PM2.5 surface. A per-interquartile range (IQR) increase in the percent of non-African American people of color was associated with a 31%, 43%, and 56% increase in the relative risk of infection, hospitalization, and mortality respectively, while a per-IQR increase in the proportion of non-Hispanic African Americans was associated with a 4% and 7% increase in the relative risk of infections and hospitalizations. The current disagreement among the different PM2.5 estimates is a key factor limiting our ability to link environmental exposures and health outcomes at the census tract level. These results have strong implications for the implementation of an equitable public health response during the crisis and suggest targeted areas for additional air monitoring in Colorado.

Differential Cardiopulmonary Health Impacts of Local and Long-Range Transport of Wildfire Smoke.

We estimated cardiopulmonary morbidity and mortality associated with wildfire smoke (WFS) fine particulate matter (PM2.5) in the Front Range of Colorado from 2010 to 2015. To estimate WFS PM2.5, we developed a daily kriged PM2.5 surface at a 15  × 15 km resolution based on the Environmental Protection Agency Air Quality System monitors for the western United States; we subtracted out local seasonal-average PM2.5 of nonsmoky days, identified using satellite-based smoke plume estimates, from the local daily estimated PM2.5 if smoke was identified by National Oceanic and Atmospheric Administration's Hazard Mapping System. We implemented time-stratified case-crossover analyses to estimate the effect of a 10 µg/m3 increase in WFS PM2.5 with cardiopulmonary hospitalizations and deaths using single and distributed lag models for lags 0-5 and distinct annual impacts based on local and long-range smoke during 2012, and long-range transport of smoke in 2015. A 10 µg/m3 increase in WFS was associated with all respiratory, asthma, and chronic obstructive pulmonary disease hospitalizations for lag day 3 and hospitalizations for ischemic heart disease at lag days 2 and 3. Cardiac arrest deaths were associated with WFS PM2.5 at lag day 0. For 2012 local wildfires, asthma hospitalizations had an inverse association with WFS PM2.5 (OR: 0.716, 95% CI: 0.517-0.993), but a positive association with WFS PM2.5 during the 2015 long-range transport event (OR: 1.455, 95% CI: 1.093-1.939). Cardiovascular mortality was associated with the 2012 long-range transport event (OR: 1.478, 95% CI: 1.124-1.944).

Spatial Surveillance of Childhood Lead Exposure in a Targeted Screening State: An Application of Generalized Additive Models in Denver, Colorado.

CONTEXT: The targeted nature of Colorado's childhood lead screening program presents several analytical issues that complicate routine epidemiologic surveillance. OBJECTIVES: To analyze spatial patterns of childhood lead exposure among children younger than 6 years, identifying areas of increased risk along with associated covariates. METHODS: We analyzed a spatial case-control data set of childhood lead poisoning using generalized additive models. Incident cases were represented by the residential locations of children younger than 6 years with confirmed elevated blood lead levels (EBLL) of 5 µg/dL or more recorded between calendar years 2010 and 2014, and controls were sampled from the population at risk. We modeled the effect of spatial location, adjusting for potential spatial confounders. We also adjusted for a number of covariates previously identified in the childhood lead poisoning literature to understand the ecologic-level drivers of spatial variation in risk. MAIN OUTCOME MEASURE(S): Crude and adjusted spatial odds ratios describing the relative frequency of lead poisoning among different locations in Denver, Colorado. RESULTS: We found evidence of statistically significant spatial clustering in incident cases of lead poisoning even after adjustment for age, sex, year, season, and spatially smoothed screening rate. Spatial confounder-adjusted odds ratios in the Denver study area ranged from 0.22 to 2.7. Adjusting for additional ecologic-level covariates effectively accounted for the observed spatial variation. We found that ecologic-level indicators of low socioeconomic status, Hispanic ethnicity, Asian race, and older housing age were all positively and significantly associated with an increased EBLL risk. CONCLUSION: Housing and socioeconomic factors continue to be the primary ecologic risk factors associated with childhood lead exposure and can be used to predict risk at a fine spatial resolution in the Denver study area. Our analysis demonstrates how other targeted screening states can be proactive about childhood lead surveillance within their major population centers and enhance the spatial specificity of lead mitigation efforts.

Development and evaluation of a pharmacogenomics educational program for pharmacists.

Objectives. To evaluate hospital and outpatient pharmacists' pharmacogenomics knowledge before and 2 months after participating in a targeted, case-based pharmacogenomics continuing education program.Design. As part of a continuing education program accredited by the Accreditation Council for Pharmacy Education (ACPE), pharmacists were provided with a fundamental pharmacogenomics education program.Evaluation. An 11-question, multiple-choice, electronic survey instrument was distributed to 272 eligible pharmacists at a single campus of a large, academic healthcare system. Pharmacists improved their pharmacogenomics test scores by 0.7 questions (pretest average 46%; posttest average 53%, p=0.0003).Conclusions. Although pharmacists demonstrated improvement, overall retention of educational goals and objectives was marginal. These results suggest that the complex topic of pharmacogenomics requires a large educational effort in order to increase pharmacists' knowledge and comfort level with this emerging therapeutic opportunity.

Assessment of the pharmacogenomics educational needs of pharmacists.

OBJECTIVES: To evaluate the self-perceived knowledge and confidence of inpatient and outpatient pharmacists in applying pharmacogenomics information to clinical practice. METHODS: A 19-question multiple-choice, electronic needs-assessment survey instrument was distributed to 480 inpatient and outpatient pharmacists in a large, academic, multi-campus healthcare system. RESULTS: The survey response rate was 64% (303). Most respondents (85%) agreed that pharmacists should be required to be knowledgeable about pharmacogenomics, and 65% agreed that pharmacists should be capable of providing information on the appropriate use of pharmacogenomics testing. Sixty-three percent felt they could not accurately apply the results of pharmacogenomics tests to drug-therapy selection, dosing, or monitoring. CONCLUSION: Pharmacists believe pharmacogenomics knowledge is important to the profession, but they lack the knowledge and self-confidence to act on the results of pharmacogenomics testing and may benefit from pharmacogenomics education.