SSNN, a method for neural network protein secondary structure fitting using circular dichroism data

Circular dichroism (CD) spectroscopy is a quick method for measuring data that can be used to determine the average secondary structures of proteins, probe their interactions with their environment, and aid in drug discovery. This paper describes the operation and testing of a self-organising map (SOM) structure-fitting methodology named Secondary Structure Neural Network (SSNN), which is a methodology for estimating protein secondary structure from CD spectra of unknown proteins using CD spectra of proteins with known X-ray structures. SSNN comes in two standalone MATLAB applications for estimating unknown proteins' structures, one that uses a pre-trained map and one that begins by training the SOM with a reference set of the user's choice. These are available at http://www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/ as SSNNGUI and SSNN1_2 respectively. They are available for both Macintosh and Windows formats with two reference sets: one obtained from the CDPro website, referred to as CDDATA.48 which has 48 protein spectra and structures, and one with 53 proteins (CDDATA.48 with 5 additional spectra). Here we compare SSNN with CDSSTR, a widely-used secondary structure methodology, and describe how to use the standalone SSNN applications. Current input format is Δε per amino acid residue from 240 nm to 190 nm in 1 nm steps for the known and unknown proteins and a vector summarising the secondary structure elements of the known proteins. The format is readily modified to include input data with e.g. extended wavelength ranges or different assignment of secondary structures

How Will Tobacco Farmers Respond to the Quota Buyout? Findings from a Survey of North Carolina Tobacco Farmers

The tobacco quota buyout is expected to have significant impacts on U.S. tobacco markets, farmers, tobacco-dependent communities, and public health. Using data from four surveys of a panel of North Carolina tobacco farmers conducted between 1997 and 2004, we investigate changing farmer attitudes towards and intentions following a quota buyout.Crop Production/Industries,

Protein secondary structure prediction from circular dichroism spectra using a self-organizing map with concentration correction

Collecting circular dichroism (CD) spectra for protein solutions is a simple experiment, yet reliable extraction of secondary structure content is dependent on knowledge of the concentration of the protein—which is not always available with accuracy. We previously developed a self-organizing map (SOM), called Secondary Structure Neural Network (SSNN), to cluster a database of CD spectra and use that map to assign the secondary structure content of new proteins from CD spectra. The performance of SSNN is at least as good as other available protein CD structure-fitting algorithms. In this work we apply SSNN to a collection of spectra of experimental samples where there was suspicion that the nominal protein concentration was incorrect. We show that by plotting the normalized root mean square deviation of the SSNN predicted spectrum from the experimental one versus a concentration scaling-factor it is possible to improve the estimate of the protein concentration while providing an estimate of the secondary structure. For our implementation (51 data points 240–190 nm in nm increments) good fits and structure estimates were obtained if the NRMSD (normalized root mean square displacement, RMSE/data range) is <0.03; reasonable for NRMSD <0.05; and variable above this. We also augmented the reference database with 100% helical spectra and truly random coil spectra

Body Satisfaction, Weight Gain, and Binge Eating Among Overweight Adolescent Girls

Objective: To examine if body satisfaction is associated with body mass index (BMI) change and whether it protects against the development of frequent binge eating among overweight and obese adolescent girls. Methods: We used prospective data from 9 waves of an ongoing cohort study of adolescents, the Growing Up Today Study. At enrollment in 1996, participants were 9 to 14 years old. Questionnaires were mailed to participants annually until 2001, then biennially through 2007. Girls who were overweight or obese in 1996 were included in the analysis (n=1 559). Our outcomes were annual change in BMI and incident frequent binge eating, defined as binge eating at least weekly and no use of compensatory behaviors. Results: At baseline, 57.2% of the overweight and obese girls were at least somewhat satisfied with their bodies. During 11 years of follow-up, 9.5% (95% confidence interval (CI) [7.8, 10.8]) of the girls started to binge eat frequently. Controlling for BMI and other confounders, overweight and obese girls who reported being at least somewhat satisfied with their bodies made smaller BMI gains (β=−0.10 kg/m$^2$, 95% CI [−0.19, −0.02]) and had 61% lower odds of starting to binge eat frequently (odds ratio (OR)=0.39, 95% CI [0.24, 0.64]) than their less satisfied peers. Compared to girls who were the least satisfied with their bodies, girls who were the most satisfied had 85% lower odds of starting to binge eat frequently (OR=0.15, 95% CI [0.06, 0.37]). The association between body satisfaction and starting to binge eat frequently was stronger for younger adolescents than older adolescents. Conclusions: While body dissatisfaction is common among overweight and obese girls, body satisfaction may protect against excessive weight gain and binge eating. Prevention of body dissatisfaction must begin early and should be considered as a component of both obesity and eating disorder prevention programs

Human Tra2 proteins jointly control a CHEK1 splicing switch among alternative and constitutive target exons

Alternative splicing—the production of multiple messenger RNA isoforms from a single gene—is regulated in part by RNA binding proteins. While the RBPs transformer2 alpha (Tra2α) and Tra2β have both been implicated in the regulation of alternative splicing, their relative contributions to this process are not well understood. Here we find simultaneous—but not individual—depletion of Tra2α and Tra2β induces substantial shifts in splicing of endogenous Tra2β target exons, and that both constitutive and alternative target exons are under dual Tra2α–Tra2β control. Target exons are enriched in genes associated with chromosome biology including CHEK1, which encodes a key DNA damage response protein. Dual Tra2 protein depletion reduces expression of full-length CHK1 protein, results in the accumulation of the DNA damage marker γH2AX and decreased cell viability. We conclude Tra2 proteins jointly control constitutive and alternative splicing patterns via paralog compensation to control pathways essential to the maintenance of cell viability

Mechanisms of attention for cues associated with rewarding and aversive outcomes

Attentional biases arising from classical conditioning processes may contribute to the maintenance of drug addictions and anxiety disorders. This thesis examined whether attentional mechanisms for conditioned stimuli (CS) would be dominated by affective properties (Lang, Greenwald, Bradley, & Hamm, 1993), or the uncertainty of the stimulus in predicting the outcome (Pearce & Hall, 1980). In chapter one affective and uncertainty-driven mechanisms of attention are discussed in relation to rewarding and aversive outcomes. In experimental chapter 2 methodological issues are addressed. In experimental chapters three and four attentional mechanisms are tested using a discriminative conditioning procedure with visual stimuli of varying predictive certainty (CS+,CS+/-,CS-) for a monetary or noise outcome (US). Attention was measured using an eye-tracker, and emotional conditioning and learning were measured using Likert scales. It was found that attention was mediated by uncertainty (chapter 3), but increasing the intensity of the outcome switched attention to affective-driven mechanisms for the noise outcome (chapter 4). In a further experiment this effect on attention remained for the noise outcome even under conditions promoting uncertainty-driven mechanisms (chapter 6). When cigarettes were the unconditioned stimuli instead of money in the appetitive conditioning, attention was also mediated by stimulus affect (chapter 5). In chapter 7 the data are discussed and it is concluded that when the outcome is highly emotionally salient, affective-driven mechanisms of attention dominate over uncertainty

Participatory politics, environmental journalism and newspaper campaigns

This is an Author's Accepted Manuscript of an article published in Journalism Studies, 13(2), 210 - 225, 2012, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/1461670X.2011.646398.This article explores the extent to which approaches to participatory politics might offer a more useful alternative to understanding the role of environmental journalism in a society where the old certainties have collapsed, only to be replaced by acute uncertainty. This uncertainty not only generates acute public anxiety about risks, it has also undermined confidence in the validity of long-standing premises about the ideal role of the media in society and journalistic professionalism. The consequence, this article argues, is that aspirations of objective reportage are outdated and ill-equipped to deal with many of the new risk stories environmental journalism covers. It is not a redrawing of boundaries that is needed but a wholesale relocation of our frameworks into approaches better suited to the socio-political conditions and uncertainties of late modernity. The exploration of participatory approaches is an attempt to suggest one way this might be done

Learner Treatment Kit (school-based malaria diagnosis and treatment in southern Malawi): Study data and support materials

A set of data collection tools, STATA .do processing scripts, and resultant datasets produced as part of the Learner Treatment Kit (LTK) Project, a study funded to evaluate the impact of a school-based programme of malaria diagnosis and treatment (malaria case management) as part of a wider school first-aid kit exploring school attendance, health and education outcomes. The study conducted a cluster randomized controlled trial in 58 primary schools in TA Chikowi, Zomba district of southern Malawi. The intervention, implemented between 2013-2015 in 29 randomly selected schools from the total of 58 schools, comprised providing free-of-charge malaria rapid diagnostic tests (RDTs) and artemisinin-based combination therapy (ACT) to primary schools to be used by trained teachers to diagnose and treat uncomplicated malaria, as part of basic first aid kits known as "Learner Treatment Kits" (LTKs). The primary outcome was school attendance, assessed through teacher-recorded school attendance registers and periodic spot checks. Secondary outcomes included prevalence of Plasmodium spp. infection, anaemia, educational performance, self-reported child wellbeing, and health seeking behaviour. The trial is registered with ClinicalTrials.gov, NCT02213211

Attitudes of Intercollegiate Athletes toward Transgender Individuals and Transgender Athletic Participation

Debate around the participation of transgender athletes in competitive sport has been increasing recently. These debates, and the discourse surrounding transgender athletes, have had wide ranging consequences, including changes to gender participation policies by sport governing bodies. While policy changes are being made, little data exists around the attitudes of athletes on the participation of transgender persons. This study explores the attitudes of intercollegiate student-athletes on transgender individuals and transgender collegiate athletic participation, using a sample of three collegiate athletic programs. Findings suggest that attitudes towards transgender persons and political ideology are significant factors in the acceptance of transgender athletic participation, particularly for trans women, while religiosity contributes to overall attitudes of transgender persons outside of sport, but not to trans athletic participation specifically

Learner Treatment Kit (school-based malaria diagnosis and treatment in southern Malawi): Study data and support materials

A set of data collection tools, STATA .do processing scripts, and resultant datasets produced as part of the Learner Treatment Kit (LTK) Project, a study funded to evaluate the impact of a school-based programme of malaria diagnosis and treatment (malaria case management) as part of a wider school first-aid kit exploring school attendance, health and education outcomes. The study conducted a cluster randomized controlled trial in 58 primary schools in TA Chikowi, Zomba district of southern Malawi. The intervention, implemented between 2013-2015 in 29 randomly selected schools from the total of 58 schools, comprised providing free-of-charge malaria rapid diagnostic tests (RDTs) and artemisinin-based combination therapy (ACT) to primary schools to be used by trained teachers to diagnose and treat uncomplicated malaria, as part of basic first aid kits known as "Learner Treatment Kits" (LTKs). The primary outcome was school attendance, assessed through teacher-recorded school attendance registers and periodic spot checks. Secondary outcomes included prevalence of Plasmodium spp. infection, anaemia, educational performance, self-reported child wellbeing, and health seeking behaviour. The trial is registered with ClinicalTrials.gov, NCT02213211