Abjection and Empathy: The Shared Spaces and Blurred Boundaries of Infinite Jest

In Infinite Jest, David Foster Wallace positions abjection in opposition to empathy. Both psychological phenomena derive from a relationship between two people, but abjection depends on a pushing away and empathy depends on a pulling toward. The experience of either phenomenon results in a blurring of interpersonal boundaries, but there is no intimacy in abjection. Instead, as made evident in the central family of Wallace’s novel, the result of abjection is that an individual retreats into the self, rejecting any attempt at intimacy that might be interpreted as an effort to breach autonomy. This alienation is best countered by empathy, as modeled in Infinite Jest in the practice of “Identification” in Alcoholics Anonymous. To identify with a person is to empathize with him or her: to share perspective and emotion. Empathy, unlike abjection, lasts only for a moment, allowing for the reinstatement of the boundaries of self

Video-based data acquisition system for use in eye blink classical conditioning procedures in sheep

Pavlovian eye blink conditioning (EBC) has been extensively studied in humans and laboratory animals, providing one of the best-understood models of learning in neuroscience. EBC has been especially useful in translational studies of cerebellar and hippocampal function. We recently reported a novel extension of EBC procedures for use in sheep, and now describe new advances in a digital video-based system. The system delivers paired presentations of conditioned stimuli (CSs; a tone) and unconditioned stimuli (USs; an air puff to the eye), or CS-alone "unpaired" trials. This system tracks the linear distance between the eyelids to identify blinks occurring as either unconditioned (URs) or conditioned (CRs) responses, to a resolution of 5 ms. A separate software application (Eye Blink Reviewer) is used to review and autoscore the trial CRs and URs, on the basis of a set of predetermined rules, permitting an operator to confirm (or rescore, if needed) the autoscore results, thereby providing quality control for accuracy of scoring. Learning curves may then be quantified in terms of the frequencies of CRs over sessions, both on trials with paired CS-US presentations and on CS-alone trials. The latency to CR onset, latency to CR peak, and occurrence of URs are also obtained. As we demonstrated in two example cases, this video-based system provides efficient automated means to conduct EBC in sheep and can facilitate fully powered studies with multigroup designs that involve paired and unpaired training. This can help extend new studies in sheep, a species well suited for translational studies of neurodevelopmental disorders resulting from gestational exposure to drugs, toxins, or intrauterine distress

Discrimination Reversal Learning in Capuchin Monkeys (Cebus apella)

Learning styles in capuchin monkeys were assessed with a computerized reversal- learning task called the mediationaJ paradigm. First, monkeys were trained to respond with 90% accuracy on a two-choice discrimination (A+B-). Then the authors examined differences in performance on three different types of reversal trials (A-B+, A-C+, B+C-), each of which offered differing predictions for performance, depending on whether the monkeys were using associative cues or rule-based strategies. Performance indicated that the monkeys mainly learned to avoid the B stimulus during training, as the A-C+ condition produced the best performance levels. Therefore, negative stimuli showed greater control over responding after reversal and reflected a more associative rather than rule-based form of learning

Trajectory Model Validation Using Newly Developed Altitude-Controlled Balloons During the International Consortium for Atmospheric Research on Transport and Transformations 2004 Campaign

During the summer of 2004, five altitude-controlled tracking balloons were flown as part of the International Consortium for Atmospheric Research on Transport and Transformations (ICARTT) campaign. These Controlled Meteorological (CMET) balloons, newly developed at the University of Massachusetts, are notable for their light weight (∼1 kg mass), efficient altitude control, case of launch, long-duration flight capability, and ability to perform repeated quasi-Lagrangian soundings. The balloons were embedded in urban plumes from New York and Boston which they tracked over New England, eastern Canada, and the Atlantic Ocean while maintaining a nearly constant altitude. The flights ranged from 10 to 111 hours and covered a maximum distance of 3000 km. Balloon flight tracks are used here to assess the accuracy of trajectory models during intensive aircraft sampling periods. A new method is presented for increasing the number of available reference trajectories by dividing the balloon flights into shorter segments for statistical analysis. For trajectory durations between 2 and 12 hours, mean trajectory errors are found to be approximately 26% and 34% of the flight distance for ECMWF-based and GFS-based trajectories, respectively. Anomalously large model errors observed during three of the flights are found to be the result of a narrow low-level jet (15 July) and synoptic-scale flow patterns (9 and 10 August). The results from this study should be useful to researchers evaluating the performance of trajectory models and chemical transport models during the ICARTT campaign. Complete CMET balloon and model trajectory data sets are available as a supplement to this paper

“I Felt Like a Superhero”: The Experience of Responding to Drug Overdose Among Individuals Trained in Overdose Prevention

BACKGROUND: Overdose prevention programs (OPPs) train people who inject drugs and other community members to prevent, recognise and respond to opioid overdose. However, little is known about the experience of taking up the role of an overdose responder for the participants. METHODS: We present findings from qualitative interviews with 30 participants from two OPPs in Los Angeles, CA, USA from 2010 to 2011 who had responded to at least one overdose since being trained in overdose prevention and response. RESULTS: Being trained by an OPP and responding to overdoses had both positive and negative effects for trained responders . Positive effects include an increased sense of control and confidence, feelings of heroism and pride, and a recognition and appreciation of one\u27s expertise. Negative effects include a sense of burden, regret, fear, and anger, which sometimes led to cutting social ties, but might also be mitigated by the increased empowerment associated with the positive effects. CONCLUSION: Findings suggest that becoming an overdose responder can involve taking up a new social role that has positive effects, but also confers some stress that may require additional support. OPPs should provide flexible opportunities for social support to individuals making the transition to this new and critical social role. Equipping individuals with the skills, technology, and support they need to respond to drug overdose has the potential to confer both individual and community-wide benefits

The Drosophila Dbf4 Ortholog Chiffon Forms A Complex with Gcn5 That Is Necessary for Histone Acetylation and Viability

Metazoans contain two homologs of the Gcn5-binding protein Ada2, Ada2a and Ada2b, which nucleate formation of the ATAC and SAGA complexes respectively. In Drosophila melanogaster, there are two splice isoforms of Ada2b: Ada2b-PA and Ada2b-PB. Here we show only the Ada2b-PB isoform is in SAGA; in contrast, Ada2b-PA associates with Gcn5, Ada3, Sgf29 and Chiffon forming the Chiffon Histone Acetyltransferase (CHAT) complex. Chiffon is theDrosophila ortholog of Dbf4, which binds and activates the cell cycle kinase Cdc7 to initiate DNA replication. In flies, Chiffon and Cdc7 are required in ovary follicle cells for gene amplification, a specialized form of DNA re-replication. Although chiffon was previously reported to be dispensable for viability, here we find that Chiffon is required for both histone acetylation and viability in flies. Surprisingly, we show that chiffon is a dicistronic gene that encodes distinct Cdc7- and CHAT-binding polypeptides. Although the Cdc7-binding domain of Chiffon is not required for viability in flies, Chiffon’s CHAT-binding domain is essential for viability but is not required for gene amplification, arguing against a role in DNA replication

Effects of dairy intake on weight maintenance

Background: To compare the effects of low versus recommended levels of dairy intake on weight maintenance and body composition subsequent to weight loss. Design and Methods: Two site (University of Kansas-KU; University of Tennessee-UT), 9 month, randomized trial. Weight loss was baseline to 3 months, weight maintenance was 4 to 9 months. Participants were maintained randomly assigned to low dairy ( 3 servings/d) diets for the maintenance phase. Three hundred thirty eight men and women, age: 40.3 ± 7.0 years and BMI: 34.5 ± 3.1, were randomized; Change in weight and body composition (total fat, trunk fat) from 4 to 9 months were the primary outcomes. Blood chemistry, blood pressure, resting metabolism, and respiratory quotient were secondary outcomes. Energy intake, calcium intake, dairy intake, and physical activity were measured as process evaluation. Results: During weight maintenance, there were no overall significant differences for weight or body composition between the low and recommended dairy groups. A significant site interaction occurred with the low dairy group at KU maintaining weight and body composition and the low dairy group at UT increasing weight and body fat. The recommended dairy group exhibited reductions in plasma 1,25-(OH)2-D while no change was observed in the low dairy group. No other differences were found for blood chemistry, blood pressure or physical activity between low and recommended dairy groups. The recommended dairy group showed significantly greater energy intake and lower respiratory quotient compared to the low dairy group. Conclusion: Weight maintenance was similar for low and recommended dairy groups. The recommended dairy group exhibited evidence of greater fat oxidation and was able to consume greater energy without greater weight gain compared to the low dairy group. Recommended levels of dairy products may be used during weight maintenance without contributing to weight gain compared to diets low in dairy products. Trial Registration: ClinicalTrials.gov NCT0068642

Disruption in A-to-I Editing Levels Affects C. elegans Development More Than a Complete Lack of Editing

A-to-I RNA editing, catalyzed by ADAR proteins, is widespread in eukaryotic transcriptomes. Studies showed that, in C. elegans, ADR-2 can actively deaminate dsRNA, whereas ADR-1 cannot. Therefore, we set out to study the effect of each of the ADAR genes on the RNA editing process. We performed comprehensive phenotypic, transcriptomics, proteomics, and RNA binding screens on worms mutated in a single ADAR gene. We found that ADR-1 mutants exhibit more-severe phenotypes than ADR-2, and some of them are a result of non-editing functions of ADR-1. We also show that ADR-1 significantly binds edited genes and regulates mRNA expression, whereas the effect on protein levels is minor. In addition, ADR-1 primarily promotes editing by ADR-2 at the L4 stage of development. Our results suggest that ADR-1 has a significant role in the RNA editing process and in altering editing levels that affect RNA expression; loss of ADR-1 results in severe phenotypes

PatternLab for proteomics: a tool for differential shotgun proteomics

<p>Abstract</p> <p>Background</p> <p>A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu <it>et al</it>. demonstrated a method to perform semi-relative protein quantitation in shotgun proteomics data by correlating the number of tandem mass spectra obtained for each protein, or "spectral count", with its abundance in a mixture; however, two issues have remained open: how to normalize spectral counting data and how to efficiently pinpoint differences between profiles. Moreover, Chen <it>et al</it>. recently showed how to increase the number of identified proteins in shotgun proteomics by analyzing samples with different MS-compatible detergents while performing proteolytic digestion. The latter introduced new challenges as seen from the data analysis perspective, since replicate readings are not acquired.</p> <p>Results</p> <p>To address the open issues above, we present a program termed PatternLab for proteomics. This program implements existing strategies and adds two new methods to pinpoint differences in protein profiles. The first method, ACFold, addresses experiments with less than three replicates from each state or having assays acquired by different protocols as described by Chen <it>et al</it>. ACFold uses a combined criterion based on expression fold changes, the AC test, and the false-discovery rate, and can supply a "bird's-eye view" of differentially expressed proteins. The other method addresses experimental designs having multiple readings from each state and is referred to as nSVM (natural support vector machine) because of its roots in evolutionary computing and in statistical learning theory. Our observations suggest that nSVM's niche comprises projects that select a minimum set of proteins for classification purposes; for example, the development of an early detection kit for a given pathology. We demonstrate the effectiveness of each method on experimental data and confront them with existing strategies.</p> <p>Conclusion</p> <p>PatternLab offers an easy and unified access to a variety of feature selection and normalization strategies, each having its own niche. Additionally, graphing tools are available to aid in the analysis of high throughput experimental data. PatternLab is available at <url>http://pcarvalho.com/patternlab</url>.</p

GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data

<p>Abstract</p> <p>Background</p> <p>Spectral counting is a shotgun proteomics approach comprising the identification and relative quantitation of thousands of proteins in complex mixtures. However, this strategy generates bewildering amounts of data whose biological interpretation is a challenge.</p> <p>Results</p> <p>Here we present a new algorithm, termed GO Explorer (GOEx), that leverages the gene ontology (GO) to aid in the interpretation of proteomic data. GOEx stands out because it combines data from protein fold changes with GO over-representation statistics to help draw conclusions. Moreover, it is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. Its usefulness is demonstrated by applying it to help interpret the effects of perillyl alcohol, a natural chemotherapeutic agent, on glioblastoma multiform cell lines (A172). We used a new multi-surfactant shotgun proteomic strategy and identified more than 2600 proteins; GOEx pinpointed key sets of differentially expressed proteins related to cell cycle, alcohol catabolism, the Ras pathway, apoptosis, and stress response, to name a few.</p> <p>Conclusion</p> <p>GOEx facilitates organism-specific studies by leveraging GO and providing a rich graphical user interface. It is a simple to use tool, specialized for biologists who wish to analyze spectral counting data from shotgun proteomics. GOEx is available at <url>http://pcarvalho.com/patternlab</url>.</p