Uncertainty and Organization Design

The task environment, characterized by the degree of complexity, variability, and routine of workers’ tasks, creates varying degrees of asymmetric information between workers and their supervisors, as well as poses varying degrees of difficulty for supervisors and workers in making correct decisions. Thus the task environment generates internal uncertainty, some of which is under the control of workers, in contrast with external uncertainty, which arises from the market and is beyond their control. The measures that address problems associated with internal uncertainty (including incentives, delegation of decision-making to workers, monitoring by supervisors and internal labor markets) are elements of organization design. We explore theoretically and empirically the relationship between uncertainty and organization design, expanding on Baker and Jorgensen’s (2003) idea that the risk-incentives relationship depends on the nature and sources of risk and Prendergast’s (2002a) idea that incentive pay is not a direct response to a firm’s task attributes but is part of a broader organization design that includes additional complementary and substitutable elements.

RNA Polymerase II during Transcript Elongation: deaiing with DNA damage and staying phosphorylated

This thesis covers two topics related to transcript elongation in Saccharomyces cerevisiae - the regulation of the phosphatase Fcp1 and transcription-coupled DNA damage repair. Formation of RNA polymerase II (RNAPII) complexes throughout the transcription cycle is mediated in part by the phosphorylation state of the C-terminal domain (CTD) of the largest RNAPII subunit. Although a multitude of kinases can phosphorylate the CTD, currently only one CTD-specific phosphatase, Fcp1, has been identified. This work studies the possibility that Fcp1 might be associated with the elongating form of RNAPII. The phosphatase co-fractionates with RNAPII in association with the elongation factor Elongator. Furthermore, genetic studies show that a double mutant that carries a deletion of an Elongator gene as well as a temperature sensitive fcp1 mutation has a synthetic lethal phenotype at the permissive temperature. In vitro assays using crude extracts demonstrate that the CTD of RNAPII becomes dephosphorylated in a Fcp1-dependent manner. In contrast, in a reconstituted DNA-RNA-RNAPII system, the addition of the purified phosphatase does not stimulate such dephosphoryation. These results indicate a close relationship between Fcp1 phosphatase and the elongating form of RNAPII. Transcription-coupled DNA damage repair is a term applied to the preferential repair of DNA damage on the coding strand within active genes. The second half of this thesis describes the characterisation of nucleotide excision repair (NER) of the intrastrand 1,3-(pGpTpG)-cisplatin lesion in Saccharomyces cerevisiae as well as an attempt to reconstitute a transcription-coupled NER reaction (TC-NER) in vitro. Using modified yeast extracts, the excision products of the above lesion by NER were found to be between 23 and 26 nucleotides long, via incisions around the 15th phosphodiester bond 3' and 7th the phosphodiester bond 5' of the damage. The attempt to reconstitute TC-NER in vitro was hindered by difficulties with the transcription substrate and the functional instability of purified NER proteins

Nanometer-sized Aerosol Particles in the Atmosphere: Measurement, Analysis, and Impact

New particle formation (NPF) from gaseous precursor vapors is frequently observed in the ambient environment and contributes to a major source of global cloud condensation nuclei (CCN). The survival and CCN activation of newly formed particles are highly dependent on particle growth below 10 nm. Characterizing and understanding nanoparticle early growth will therefore help to quantify the impact of NPF on cloud reflectivity and global energy budget. In this work, I first present a recently developed instrument, the Caltech nano-Scanning Electrical Mobility Spectrometer (nSEMS), which consists of a charge conditioner, a novel differential mobility analyzer (DMA), and a two-stage condensation particle counter (CPC). This new design, coupled with a data inversion method that combines empirical calibration and COMSOL simulation, can help to measure nanoparticle size distributions from 1.5 nm to 25 nm more accurately. This instrument was employed in the experiments conducted in the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber at the European Organization for Nuclear Research (CERN) to better understand NPF, particle growth and survival. Multiple experimental parameters were varied to study the influence of different highly oxygenated molecules (HOMs) and inorganic trace gases, such as ammonia and nitrogen oxides on particle early growth. Experiment results have suggested a novel mechanism that may help to explain nanoparticle formation and growth in highly polluted urban environments or in the cold free troposphere. In as little as a few minutes, freshly nucleated particles as small as 2 nanometers in diameter can grow very rapidly due to simultaneous condensation of nitric acid and ammonia. This can help them to survive through the so-called "valley of death" where they would otherwise be lost to larger particles, and instead allow them to grow to sizes where they are less vulnerable to loss and can continue on to sizes where they influence local air quality or climate. Further, the laboratory results of nanoparticle growth were incorporated into the Global Model of Aerosol Processes (GLOMAP) model to study the impact of this extremely rapid growth on the global CCN budget. Having realized the importance of conducting well-controlled chamber experiments and of using chamber experimental data, we established an online data infrastructure, the Index of Chamber Atmospheric Research in the United States (ICARUS), for storing, sharing, and using chamber data. A combined effort of the described works contributes to better measuring the size distribution of nanoparticles and to understanding their impact on global climate.</p

Methodological review: quality of randomized controlled trials in health literacy

Background: The growing move towards patient-centred care has led to substantial research into improving the health literacy skills of patients and members of the public. Hence, there is a pressing need to assess the methodology used in contemporary randomized controlled trials (RCTs) of interventions directed at health literacy, in particular the quality (risk of bias), and the types of outcomes reported. Methods: We conducted a systematic database search for RCTs involving interventions directed at health literacy in adults, published from 2009 to 2014. The Cochrane Risk of Bias tool was used to assess quality of RCT implementation. We also checked the sample size calculation for primary outcomes. Reported evidence of efficacy (statistical significance) was extracted for intervention outcomes in any of three domains of effect: knowledge, behaviour, health status. Demographics of intervention participants were also extracted, including socioeconomic status. Results: We found areas of methodological strength (good randomization and allocation concealment), but areas of weakness regarding blinding of participants, people delivering the intervention and outcomes assessors. Substantial attrition (losses by monitoring time point) was seen in a third of RCTs, potentially leading to insufficient power to obtain precise estimates of intervention effect on primary outcomes. Most RCTs showed that the health literacy interventions had some beneficial effect on knowledge outcomes, but this was typically for less than 3 months after intervention end. There were far fewer reports of significant improvements in substantive patient-oriented outcomes, such as beneficial effects on behavioural change or health (clinical) status. Most RCTs featured participants from vulnerable populations. Conclusions: Our evaluation shows that health literacy trial design, conduct and reporting could be considerably improved, particularly by reducing attrition and obtaining longer follow-up. More meaningful RCTs would also result if health literacy trials were designed with public and patient involvement to focus on clinically important patient-oriented outcomes, rather than just knowledge, behaviour or skills in isolation

Comparison of two- and three-dimensional methods for analysis of trunk kinematic variables in the golf swing

This is the as accepted for publication version of a paper subsequently published in the Journal of Applied Biomechanics © Human Kinetics. The definitive version is available at: http://dx.doi.org/10.1123/jab.2015-0032Two-dimensional methods have been used to compute trunk kinematic variables (flexion/extension, lateral bend, axial rotation) and X-factor (difference in axial rotation between trunk and pelvis) during the golf swing. Recent X-factor studies advocated three-dimensional (3D) analysis due to the errors associated with two-dimensional (2D) methods, but this has not been investigated for all trunk kinematic variables. The purpose of this study was to compare trunk kinematic variables and X-factor calculated by 2D and 3D methods to examine how different approaches influenced their profiles during the swing. Trunk kinematic variables and X-factor were calculated for golfers from vectors projected onto the global laboratory planes and from 3D segment angles. Trunk kinematic variable profiles were similar in shape; however, there were statistically significant differences in trunk flexion (-6.5 ± 3.6°) at top of backswing and trunk right-side lateral bend (8.7 ± 2.9°) at impact. Differences between 2D and 3D X-factor (approximately 16°) could largely be explained by projection errors introduced to the 2D analysis through flexion and lateral bend of the trunk and pelvis segments. The results support the need to use a 3D method for kinematic data calculation to accurately analyze the golf swing

Identification of Mammalian Mediator Subunits with Similarities to Yeast Mediator Subunits Srb5, Srb6, Med11, and Rox3

The Mediator is a multiprotein coactivator required for activation of RNA polymerase II transcription by DNA binding transactivators. We recently identified a mammalian homologue of yeast Mediator subunit Med8 and partially purified a Med8-containing Mediator complex from rat liver nuclei (Brower, C. S., Sato, S., Tomomori-Sato, C., Kamura, T., Pause, A., Stearman, R., Klausner, R. D., Malik, S., Lane, W. S., Sorokina, I., Roeder, R. G., Conaway, J. W., and Conaway, R. C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10353-10358). Analysis of proteins present in the most highly purified Med8-containing fractions by tandem mass spectrometry led to the identification of many known mammalian Mediator subunits, as well as four potential Mediator subunits exhibiting sequence similarity to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. Here we present direct biochemical evidence that these four proteins are bona fide mammalian Mediator subunits. In addition, we identify direct pairwise binding partners of these proteins among the known mammalian Mediator subunits. Taken together, our findings identify a collection of novel mammalian Mediator subunits and shed new light on the underlying architecture of the mammalian Mediator complex

Moving Beyond the Colors: The Full Life-Cycle Emissions of Hydrogen Production Pathways for California

There is growing interest in the use of hydrogen as a transportation fuel but the environmental benefits of using hydrogen depend critically on how it is produced and distributed. Leading alternatives to using fossil natural gas to make hydrogen through the conventional method of steam methane reforming include using electrolyzers to split water into hydrogen and oxygen, and the use of biogas as an alternative feedstock to fossil natural gas. This report examines the latest carbon intensity (CI) estimates for these and various other hydrogen production processes, adding important nuances to the general “colors of hydrogen” scheme that has been used in recent years. CI values for hydrogen production can vary widely both within and across hydrogen production pathways. The lowest CI pathways use biomass or biogas as a feedstock, and solar or wind power. The report also analyses jobs creation from new hydrogen production facilities and shows that these benefits can be significant for large-scale facilities based on either future biomass/biogas-to-hydrogen or solar-hydrogen production technologies. Recommendations include setting stricter goals for the state’s Low Carbon Fuel Standard (LCFS) program to continue to reduce the carbon footprint of California’s transportation fuels

Activation of p53-regulated pro-apoptotic signaling pathways in PrP-mediated myopathy

<p>Abstract</p> <p>Background</p> <p>We have reported that doxycycline-induced over-expression of wild type prion protein (PrP) in skeletal muscles of Tg(HQK) mice is sufficient to cause a primary myopathy with no signs of peripheral neuropathy. The preferential accumulation of the truncated PrP C1 fragment was closely correlated with these myopathic changes. In this study we use gene expression profiling to explore the temporal program of molecular changes underlying the PrP-mediated myopathy.</p> <p>Results</p> <p>We used DNA microarrays, and confirmatory real-time PCR and Western blot analysis to demonstrate deregulation of a large number of genes in the course of the progressive myopathy in the skeletal muscles of doxycycline-treated Tg(HQK) mice. These include the down-regulation of genes coding for the myofibrillar proteins and transcription factor MEF2c, and up-regulation of genes for lysosomal proteins that is concomitant with increased lysosomal activity in the skeletal muscles. Significantly, there was prominent up-regulation of p53 and p53-regulated genes involved in cell cycle arrest and promotion of apoptosis that paralleled the initiation and progression of the muscle pathology.</p> <p>Conclusion</p> <p>The data provides the first <it>in vivo </it>evidence that directly links p53 to a wild type PrP-mediated disease. It is evident that several mechanistic features contribute to the myopathy observed in PrP over-expressing mice and that p53-related apoptotic pathways appear to play a major role.</p