High-throughput discovery of post-transcriptional cis-regulatory elements

Validation of 8mers found in the main screen. (PDF 280 kb

Open Collaboration: A Problem Solving Strategy That Is Redefining NASA's Innovative Spirit

In 2010, NASA?s Space Life Sciences Directorate announced the successful results from pilot experiments with open innovation methodologies. Specifically, utilization of internet based external crowd sourcing platforms to solve challenging problems in human health and performance related to the future of spaceflight. The follow-up to this success was an internal crowd sourcing pilot program entitled NASA@work, which was supported by the InnoCentive@work software platform. The objective of the NASA@work pilot was to connect the collective knowledge of individuals from all areas within the NASA organization via a private web based environment. The platform provided a venue for NASA Challenge Owners, those looking for solutions or new ideas, to pose challenges to internal solvers, those within NASA with the skill and desire to create solutions. The pilot was launched in 57 days, a record for InnoCentive and NASA, and ran for three months with a total of 20 challenges posted Agency wide. The NASA@work pilot attracted over 6000 participants throughout NASA with a total of 183 contributing solvers for the 20 challenges posted. At the time of the pilot?s closure, solvers provided viable solutions and ideas for 17 of the 20 posted challenges. The solver community provided feedback on the pilot describing it as a barrier breaking activity, conveying that there was a satisfaction associated with helping co-workers, that it was "fun" to think about problems outside normal work boundaries, and it was nice to learn what challenges others were facing across the agency. The results and the feedback from the solver community have demonstrated the power and utility of an internal collaboration tool, such as NASA@work

Learning to Lead Group Discussions: Teacher Education at the Intersection of Content, Pedagogy, and Equity

In this paper, five teacher educators explore the integration of practice-based teacher education pedagogies to support preservice teacher learning and enactment of large group discussion in fieldwork settings. We discuss our own insights into the shifts in our instruction as we focus more acutely on teaching high leverage practices through practice-based teacher education pedagogies. We share the units we taught with specific focus on the intersecting and overlapping knowledge related to content, pedagogy, and equity necessary for effective teaching through large group discussions. We discuss tensions that arose in our own practice and offer implications for teacher educators interested in shifting towards practice-based teacher education to support preservice teacher learning

Relief of chronic pain associated with increase in midline frontal theta power

INTRODUCTION: There is a need to identify objective cortical electrophysiological correlates for pain relief that could potentially contribute to a better pain management. However, the field of developing brain biomarkers for pain relief is still largely underexplored. OBJECTIVES: The objective of this study was to investigate cortical electrophysiological correlates associated with relief from chronic pain. Those features of pain relief could serve as potential targets for novel therapeutic interventions to treat pain. METHODS: In 12 patients with chronic pain in the upper or lower extremity undergoing a clinically indicated nerve block procedure, brain activity was recorded by means of electroencephalogram before and 30 minutes after the nerve block procedure. To determine the specific cortical electrophysiological correlates of relief from chronic pain, 12 healthy participants undergoing cold-pressor test to induce experimental acute pain were used as a control group. The data were analyzed to characterize power spectral density patterns of pain relief and identify their source generators at cortical level. RESULTS: Chronic pain relief was associated with significant delta, theta, and alpha power increase at the frontal area. However, only midfrontal theta power increase showed significant positive correlation with magnitude of reduction in pain intensity. The sources of theta power rebound were located in the left dorsolateral prefrontal cortex (DLPFC) and midline frontal cortex. Furthermore, theta power increase in the midline frontal cortex was significantly higher with chronic vs acute pain relief. CONCLUSION: These findings may provide basis for targeting chronic pain relief via modulation of the midline frontal theta oscillations

A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve

Abstract Background Identifying functional non-coding variation is critical for defining the genetic contributions to human disease. While single-nucleotide polymorphisms (SNPs) within cis-acting transcriptional regulatory elements have been implicated in disease pathogenesis, not all cell types have been assessed and functional validations have been limited. In particular, the cells of the peripheral nervous system have been excluded from genome-wide efforts to link non-coding SNPs to altered gene function. Addressing this gap is essential for defining the genetic architecture of diseases that affect the peripheral nerve. We developed a computational pipeline to identify SNPs that affect regulatory function (rSNPs) and evaluated our predictions on a set of 144 regions in Schwann cells, motor neurons, and muscle cells. Results We identified 28 regions that display regulatory activity in at least one cell type and 13 SNPs that affect regulatory function. We then tailored our pipeline to one peripheral nerve cell type by incorporating SOX10 ChIP-Seq data; SOX10 is essential for Schwann cells. We prioritized 22 putative SOX10 response elements harboring a SNP and rapidly validated two rSNPs. We then selected one of these elements for further characterization to assess the biological relevance of our approach. Deletion of the element from the genome of cultured Schwann cells—followed by differential gene expression studies—revealed Tubb2b as a candidate target gene. Studying the enhancer in developing mouse embryos revealed activity in SOX10-positive cells including the dorsal root ganglia and melanoblasts. Conclusions Our efforts provide insight into the utility of employing strict conservation for rSNP discovery. This strategy, combined with functional analyses, can yield candidate target genes. In support of this, our efforts suggest that investigating the role of Tubb2b in SOX10-positive cells may reveal novel biology within these cell populations.https://deepblue.lib.umich.edu/bitstream/2027.42/143511/1/12864_2018_Article_4692.pd

The practical implications of using standardized estimation equations in calculating the prevalence of chronic kidney disease

BACKGROUND: Kidney Disease Outcomes Quality Initiative (KDOQI) chronic kidney disease (CKD) guidelines have focused on the utility of using the modified four-variable MDRD equation (now traceable by isotope dilution mass spectrometry IDMS) in calculating estimated glomerular filtration rates (eGFRs). This study assesses the practical implications of eGFR correction equations on the range of creatinine assays currently used in the UK and further investigates the effect of these equations on the calculated prevalence of CKD in one UK regionMETHODS: Using simulation, a range of creatinine data (30-300 micromol/l) was generated for male and female patients aged 20-100 years. The maximum differences between the IDMS and MDRD equations for all 14 UK laboratory techniques for serum creatinine measurement were explored with an average of individual eGFRs calculated according to MDRD and IDMS &lt; 60 ml/min/1.73 m(2) and 30 ml/min/1.73 m(2). Similar procedures were applied to 712,540 samples from patients &gt; or = 18 years (reflecting the five methods for serum creatinine measurement utilized in Northern Ireland) to explore, graphically, maximum differences in assays. CKD prevalence using both estimation equations was compared using an existing cohort of observed data.RESULTS: Simulated data indicates that the majority of laboratories in the UK have small differences between the IDMS and MDRD methods of eGFR measurement for stages 4 and 5 CKD (where the averaged maximum difference for all laboratory methods was 1.27 ml/min/1.73 m(2) for females and 1.59 ml/min/1.73 m(2) for males). MDRD deviated furthest from the IDMS results for the Endpoint Jaffe method: the maximum difference of 9.93 ml/min/1.73 m(2) for females and 5.42 ml/min/1.73 m(2) for males occurred at extreme ages and in those with eGFR &gt; 30 ml/min/1.73 m(2). Observed data for 93,870 patients yielded a first MDRD eGFR &lt; 60 ml/min/1.73 m(2) in 2001. 66,429 (71%) had a second test &gt; 3 months later of which 47,093 (71%) continued to have an eGFR &lt; 60 ml/min/1.73 m(2). Estimated crude prevalence was 3.97% for laboratory detected CKD in adults using the MDRD equation which fell to 3.69% when applying the IDMS equation. Over 95% of this difference in prevalence was explained by older females with stage 3 CKD (eGFR 30-59 ml/min/1.73 m(2)) close to the stage 2 CKD (eGFR 60-90 ml/min/1.73 m(2)) interface.CONCLUSIONS: Improved accuracy of eGFR is obtainable by using IDMS correction especially in the earlier stages of CKD 1-3. Our data indicates that this improved accuracy could lead to reduced prevalence estimates and potentially a decreased likelihood of onward referral to nephrology services particularly in older females.</p

Factors associated with choice of intensification treatment for type 2 diabetes after metformin monotherapy: a cohort study in UK primary care.

PURPOSE: To understand the patient characteristics associated with treatment choice at the first treatment intensification for type 2 diabetes. PATIENTS AND METHODS: This is a noninterventional study, using UK electronic primary care records from the Clinical Practice Research Datalink. We included adults treated with metformin monotherapy between January 2000 and July 2017. The outcome of interest was the drug prescribed at first intensification between 2014 and 2017. We used multinomial logistic regression to calculate the ORs for associations between the drugs and patient characteristics. RESULTS: In total, 14,146 people started treatment with an intensification drug. Younger people were substantially more likely to be prescribed sodium-glucose co-transporter-2 inhibitors (SGLT2is), than sulfonylureas (SUs): OR for SGLT2i prescription for those aged <30 years was 2.47 (95% CI 1.39-4.39) compared with those aged 60-70 years. Both overweight and obesity were associated with greater odds of being prescribed dipeptidyl peptidase-4 inhibitor (DPP4i) or SGLT2i. People of non-white ethnicity were less likely to be prescribed SGLT2i or DPP4i: compared with white patients, the OR of being prescribed SGLT2i among South Asians is 0.60 (95% CI 0.42-0.85), and for black people, the OR is 0.54 (95% CI 0.30-0.97). Lower socioeconomic status was also independently associated with reduced odds of being prescribed SGLT2is. CONCLUSION: Both clinical and demographic factors are associated with prescribing at the first stage of treatment intensification, with older and non-white people less likely to receive new antidiabetic treatments. Our results suggest that the selection of treatment options used at the first stage of treatment intensification for type 2 diabetes is not driven by clinical need alone

Translatomic analysis of regenerating and degenerating spinal motor neurons in injury and ALS

The neuromuscular junction is a synapse critical for muscle strength and coordinated motor function. Unlike CNS injuries, motor neurons mount robust regenerative responses after peripheral nerve injuries. Conversely, motor neurons selectively degenerate in diseases such as amyotrophic lateral sclerosis (ALS). To assess how these insults affect motor neurons in vivo, we performed ribosomal profiling of mouse motor neurons. Motor neuron-specific transcripts were isolated from spinal cords following sciatic nerve crush, a model of acute injury and regeneration, and in the SOD1G93A ALS model. Of the 267 transcripts upregulated after nerve crush, 38% were also upregulated in SOD1G93A motor neurons. However, most upregulated genes in injured and ALS motor neurons were context specific. Some of the most significantly upregulated transcripts in both paradigms were chemokines such as Ccl2 and Ccl7, suggesting an important role for neuroimmune modulation. Collectively these data will aid in defining pro-regenerative and pro-degenerative mechanisms in motor neurons

Comparative effects of sulphonylureas, dipeptidyl peptidase-4 inhibitors and sodium-glucose co-transporter-2 inhibitors added to metformin monotherapy: a propensity-score matched cohort study in UK primary care.

AIM: To assess the comparative effects of sodium-glucose co-transporter-2 (SGLT2) inhibitors, sulphonylureas (SUs) and dipeptidyl peptidase-4 (DPP-4) inhibitors on cardiometabolic risk factors in routine care. MATERIALS AND METHODS: Using primary care data on 10?631 new users of SUs, SGLT2 inhibitors or DPP-4 inhibitors added to metformin, obtained from the UK Clinical Practice Research Datalink, we created propensity-score matched cohorts and used linear mixed models to describe changes in glycated haemoglobin (HbA1c), estimated glomerular filtration rate (eGFR), systolic blood pressure (BP) and body mass index (BMI) over 96?weeks. RESULTS: HbA1c levels fell substantially after treatment intensification for all drugs: mean change at week 12: SGLT2 inhibitors: -15.2?mmol/mol (95% confidence interval [CI] -16.9, -13.5); SUs: -14.3?mmol/mol (95% CI -15.5, -13.2); and DPP-4 inhibitors: -11.9?mmol/mol (95% CI -13.1, -10.6). Systolic BP fell for SGLT2 inhibitor users throughout follow-up, but not for DPP-4 inhibitor or SU users: mean change at week 12: SGLT2 inhibitors: -2.3?mmHg (95% CI -3.8, -0.8); SUs: -0.8?mmHg (95% CI -1.9, +0.4); and DPP-4 inhibitors: -0.9?mmHg (95% CI -2.1,+0.2). BMI decreased for SGLT2 inhibitor and DPP-4 inhibitor users, but not SU users: mean change at week 12: SGLT2 inhibitors: -0.7?kg/m2 (95% CI -0.9, -0.5); SUs: 0.0?kg/m2 (95% CI -0.3, +0.2); and DPP-4 inhibitors: -0.3?kg/m2 (95% CI -0.5, -0.1). eGFR fell at 12?weeks for SGLT2 inhibitor and DPP-4 inhibitor users. At 60?weeks, the fall in eGFR from baseline was similar for each drug class. CONCLUSIONS: In routine care, SGLT2 inhibitors had greater effects on cardiometabolic risk factors than SUs. Routine care data closely replicated the effects of diabetes drugs on physiological variables measured in clinical trials

Designing count‐based studies in a world of hierarchical models

Abstract: Advances in hierarchical modeling have improved estimation of ecological parameters from count data, especially those quantifying population abundance, distribution, and dynamics by explicitly accounting for observation processes, particularly incomplete detection. Even hierarchical models that account for incomplete detection, however, cannot compensate for data limitations stemming from poorly planned sampling. Ecologists therefore need guidance for planning count‐based studies that follow established sampling theory, collect appropriate data, and apply current modeling approaches to answer their research questions. We synthesize available literature relevant to guiding count‐based studies. Considering the central historical and ongoing contributions of avian studies to ecological knowledge, we focus on birds as a case study for this review, but the basic principles apply to all populations whose members are sufficiently observable to be counted. The sequence of our review represents the thought process in which we encourage ecologists to engage 1) the research question(s) and population parameters to measure, 2) sampling design, 3) analytical framework, 4) temporal design, and 5) survey protocol. We also provide 2 hypothetical demonstrations of these study plan components representing different research questions and study systems. Mirroring the structure of hierarchical models, we suggest researchers primarily focus on the ecological processes of interest when designing their approach to sampling, and wait to consider logistical constraints of data collection and observation processes when developing the survey protocol. We offer a broad framework for researchers planning count‐based studies, while pointing to relevant literature elaborating on particular tools and concepts