Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association

Transcription factors (TFs) are fundamental controllers of cellular regulation that function in a complex and combinatorial manner. Accurate identification of a transcription factor's targets is essential to understanding the role that factors play in disease biology. However, due to a high false positive rate, identifying coherent functional target sets is difficult. We have created an improved mapping of targets by integrating ChIP-Seq data with 423 functional modules derived from 9,395 human expression experiments. We identified 5,002 TF-module relationships, significantly improved TF target prediction, and found 30 high-confidence TF-TF associations, of which 14 are known. Importantly, we also connected TFs to diseases through these functional modules and identified 3,859 significant TF-disease relationships. As an example, we found a link between MEF2A and Crohn's disease, which we validated in an independent expression dataset. These results show the power of combining expression data and ChIP-Seq data to remove noise and better extract the associations between TFs, functional modules, and disease

Tool for Torquing Circular Electrical-Connector Collars

An improved tool has been devised for applying torque to lock and unlock knurled collars on circular electrical connectors. The tool was originally designed for, and used by, astronauts working in outer space on the Hubble Space Telescope (HST). The tool is readily adaptable to terrestrial use in installing and removing the same or similar circular electrical connectors as well as a wide variety of other cylindrical objects, the tightening and loosening of which entail considerable amounts of torque

Faculty perceptions of a tobacco cessation train-the-trainer workshop and experiences with implementation: A qualitative follow-up study

Background Between 2003 and 2005, pharmacy faculty members (n = 191) participated in a national train-the-trainer workshop designed to equip faculty with the necessary knowledge and skills to implement a shared curriculum, Rx for Change: Clinician-Assisted Tobacco Cessation, at pharmacy schools across the United States. Objective To conduct a long-term, qualitative follow-up study of faculty participants to describe (a) perceptions of the train-the-trainer workshop, and (b) subsequent experiences with curricular implementation. Results of this investigation will inform a national survey of all train-the-trainer participants. Methods Participants were selected via random sampling from the group of 191 faculty members who participated in the workshop. Semi-structured telephone interviews with participants were audio-recorded and transcribed, and qualitative thematic analysis was conducted. Results Eighteen (62%) of 29 invited individuals participated in the interviews. All participants reported implementing components of Rx for Change at their institution. The analysis yielded eight major themes pertaining to faculty perceptions and experiences with implementation: (1) accessibility to tools for teaching, (2) increased confidence and skills, (3) flexibility delivering the curriculum, (4) factors facilitating implementation and challenges encountered by faculty, (5) enhancement in treating tobacco users in clinical practice, (6) students' confidence and cognizance of the pharmacists' role as a public health advocate, (7) networking and career development opportunities, and (8) useful background for research. Conclusion Participation in the train-the-trainer workshop increased self-reported confidence for teaching tobacco cessation, and faculty valued access to useful, updated tools for teaching. Furthermore, their newly acquired counseling skills were deemed helpful for treating patients' tobacco use and dependence in clinical practice. Participants also perceived improved pharmacy students' confidence and beneficial networking opportunities. Results can help future trainers understand faculty experiences with implementing a shared, national curriculum and inform faculty participants of some of the potential long-term outcomes as a result of participation

Examining if being overweight really confers protection against dementia: Sixty-four year follow-up of participants in the Glasgow University alumni cohort study

BACKGROUND: Recent large-scale studies suggest that obesity and overweight may confer protection against future dementia. This observation could, however, be generated by reverse causality. That is, weight loss in the incipient phase of dementia ascribed to diminished self-care, including sub-optimal nutrition, would have the effect of generating such an inverse association. One approach to circumventing this problem would be to measure weight in a population which is young enough to be free of the symptoms of dementia which is then followed up for dementia occurrence over many decades. METHODS: In a prospective cohort study, body mass index, and other potential risk factors, were measured in 9547 male university undergraduates (mean age 20.5 years) in 1948-68 who were then linked to national mortality registers. RESULTS: Of 2537 deaths over a mean of 50.6 years follow up, 140 were ascribed to dementia. There was no association between overweight and future dementia deaths (age-adjusted hazard ratio; 95 % confidence interval: 0.93; 0.49, 1.79). CONCLUSION: In this cohort study of former university students, being overweight in youth did not confer protection against later dementia death

Achieving high-sensitivity for clinical applications using augmented exome sequencing

daSNVs in ACMG genes where inadequate coverage was observed among at least one platform, using WES/ACE data normalized to both 12 Gb and 100× mean coverage. (XLSX 312 kb

Impact of seasonal variation, age and smoking status on human semen parameters: The Massachusetts General Hospital experience

BACKGROUND: To investigate the relationship of human semen parameters with season, age and smoking status. METHODS: The present study used data from subjects recruited into an ongoing cross-sectional study on the relationship between environmental agents and semen characteristics. Our population consisted of 306 patients who presented to the Vincent Memorial Andrology Laboratory of Massachusetts General Hospital for semen evaluation. Sperm concentration and motility were measured with computer aided sperm analysis (CASA). Sperm morphology was scored using Tygerberg Kruger strict criteria. Regression analyses were used to investigate the relationships between semen parameters and season, age and smoking status, adjusting for abstinence interval. RESULTS: Sperm concentration in the spring was significantly higher than in winter, fall and summer (p < 0.05). There was suggestive evidence of higher sperm motility and percent of sperm with normal morphology in the spring than in the other seasons. There were no statistically significant relationships between semen parameters and smoking status, though current smokers tended to have lower sperm concentration. We also did not find a statistically significant relationship between age and semen parameters. CONCLUSIONS: We found seasonal variations in sperm concentration and suggestive evidence of seasonal variation in sperm motility and percent sperm with normal morphology. Although smoking status was not a significant predictor of semen parameters, this may have been due to the small number of current smokers in the study

An interplanetary shock traced by planetary auroral storms from the Sun to Saturn

A relationship between solar activity and aurorae on Earth was postulated(1,2) long before space probes directly detected plasma propagating outwards from the Sun(3). Violent solar eruption events trigger interplanetary shocks(4) that compress Earth's magnetosphere, leading to increased energetic particle precipitation into the ionosphere and subsequent auroral storms(5,6). Monitoring shocks is now part of the 'Space Weather' forecast programme aimed at predicting solar-activity-related environmental hazards. The outer planets also experience aurorae, and here we report the discovery of a strong transient polar emission on Saturn, tentatively attributed to the passage of an interplanetary shock - and ultimately to a series of solar coronal mass ejection (CME) events. We could trace the shock-triggered events from Earth, where auroral storms were recorded, to Jupiter, where the auroral activity was strongly enhanced, and to Saturn, where it activated the unusual polar source. This establishes that shocks retain their properties and their ability to trigger planetary auroral activity thoughout the Solar System. Our results also reveal differences in the planetary auroral responses on the passing shock, especially in their latitudinal and local time dependences.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62930/1/nature02986.pd

Partial Volume Correction in Quantitative Amyloid Imaging.

Amyloid imaging is a valuable tool for research and diagnosis in dementing disorders. As positron emission tomography (PET) scanners have limited spatial resolution, measured signals are distorted by partial volume effects. Various techniques have been proposed for correcting partial volume effects, but there is no consensus as to whether these techniques are necessary in amyloid imaging, and, if so, how they should be implemented. We evaluated a two-component partial volume correction technique and a regional spread function technique using both simulated and human Pittsburgh compound B (PiB) PET imaging data. Both correction techniques compensated for partial volume effects and yielded improved detection of subtle changes in PiB retention. However, the regional spread function technique was more accurate in application to simulated data. Because PiB retention estimates depend on the correction technique, standardization is necessary to compare results across groups. Partial volume correction has sometimes been avoided because it increases the sensitivity to inaccuracy in image registration and segmentation. However, our results indicate that appropriate PVC may enhance our ability to detect changes in amyloid deposition