Modeling Symmetric Macromolecular Structures in Rosetta3

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems

Under pressure: Response urgency modulates striatal and insula activity during decision-making under risk

When deciding whether to bet in situations that involve potential monetary loss or gain (mixed gambles), a subjective sense of pressure can influence the evaluation of the expected utility associated with each choice option. Here, we explored how gambling decisions, their psychophysiological and neural counterparts are modulated by an induced sense of urgency to respond. Urgency influenced decision times and evoked heart rate responses, interacting with the expected value of each gamble. Using functional MRI, we observed that this interaction was associated with changes in the activity of the striatum, a critical region for both reward and choice selection, and within the insula, a region implicated as the substrate of affective feelings arising from interoceptive signals which influence motivational behavior. Our findings bridge current psychophysiological and neurobiological models of value representation and action-programming, identifying the striatum and insular cortex as the key substrates of decision-making under risk and urgency

Winter marine atmospheric conditions over the Japan Sea

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 109 (2004): C12011, doi:10.1029/2001JC001197.Four basic types of synoptic-scale conditions describe the atmospheric structure and variability observed over the Japan Sea during the 1999/2000 winter season: (1) flow of cold Asian air from the northwest, (2) an outbreak of very cold Siberian air from the north and northeast, (3) passage of a weak cyclone over the southern Japan Sea with a cold air outbreak on the backside of the low, and (4) passage of a moderate cyclone along the northwestern side of the Japan Sea. In winter, the Russian coastal mountains and a surface-air temperature inversion typically block cold surface continental air from the Japan Sea. Instead, the adiabatic warming of coastal mountain lee-side air results in small air-sea temperature differences. Occasional outbreaks of very cold Siberian air eliminate the continental surface-based inversion and stability, allowing very cold air to push out over the Japan Sea for 1–3 days. During these outbreaks, the 0°C surface air isotherm extends well southward of 40°N, the surface heat losses in the center of the Japan Sea can exceed 600 W m−2, and sheet clouds cover most of the Japan Sea, with individual roll clouds extending from near the Russian coast to Honshu. During December through February, 1991–2002, these strong cold-air outbreak conditions occur 39% of the time and contribute 43% of the net heat loss from the Japan Sea. The average number of strong cold-air events per winter (November–March) season is 13 (ranging from 5 to 19); the 1999/2000 winter season covered in our measurements was normal.Support for this program was provided by the Office of Naval Research through grants N00014-98-1-0345, N00014-99-1- 0205, and N00014-98-1-0210

Designer cell signal processing circuits for biotechnology

Microorganisms are able to respond effectively to diverse signals from their environment and internal metabolism owing to their inherent sophisticated information processing capacity. A central aim of synthetic biology is to control and reprogramme the signal processing pathways within living cells so as to realise repurposed, beneficial applications ranging from disease diagnosis and environmental sensing to chemical bioproduction. To date most examples of synthetic biological signal processing have been built based on digital information flow, though analogue computing is being developed to cope with more complex operations and larger sets of variables. Great progress has been made in expanding the categories of characterised biological components that can be used for cellular signal manipulation, thereby allowing synthetic biologists to more rationally programme increasingly complex behaviours into living cells. Here we present a current overview of the components and strategies that exist for designer cell signal processing and decision making, discuss how these have been implemented in prototype systems for therapeutic, environmental, and industrial biotechnological applications, and examine emerging challenges in this promising field

Psychophysiological Correlates of Sexually and Non-Sexually Motivated Attention to Film Clips in a Workload Task

Some authors have speculated that the cognitive component (P3) of the Event-Related Potential (ERP) can function as a psychophysiological measure of sexual interest. The aim of this study was to determine if the P3 ERP component in a workload task can be used as a specific and objective measure of sexual motivation by comparing the neurophysiologic response to stimuli of motivational relevance with different levels of valence and arousal. A total of 30 healthy volunteers watched different films clips with erotic, horror, social-positive and social-negative content, while answering an auditory oddball paradigm. Erotic film clips resulted in larger interference when compared to both the social-positive and auditory alone conditions. Horror film clips resulted in the highest levels of interference with smaller P3 amplitudes than erotic and also than social-positive, social-negative and auditory alone condition. No gender differences were found. Both horror and erotic film clips significantly decreased heart rate (HR) when compared to both social-positive and social-negative films. The erotic film clips significantly increased the skin conductance level (SCL) compared to the social-negative films. The horror film clips significantly increased the SCL compared to both social-positive and social-negative films. Both the highly arousing erotic and non-erotic (horror) movies produced the largest decrease in the P3 amplitude, a decrease in the HR and an increase in the SCL. These data support the notion that this workload task is very sensitive to the attentional resources allocated to the film clip, although they do not act as a specific index of sexual interest. Therefore, the use of this methodology seems to be of questionable utility as a specific measure of sexual interest or as an objective measure of the severity of Hypoactive Sexual Desire Disorder

Protein trafficking through the endosomal system prepares intracellular parasites for a home invasion

Toxoplasma (toxoplasmosis) and Plasmodium (malaria) use unique secretory organelles for migration, cell invasion, manipulation of host cell functions, and cell egress. In particular, the apical secretory micronemes and rhoptries of apicomplexan parasites are essential for successful host infection. New findings reveal that the contents of these organelles, which are transported through the endoplasmic reticulum (ER) and Golgi, also require the parasite endosome-like system to access their respective organelles. In this review, we discuss recent findings that demonstrate that these parasites reduced their endosomal system and modified classical regulators of this pathway for the biogenesis of apical organelles

Socioeconomic disparities in breast cancer survival: relation to stage at diagnosis, treatment and race

<p>Abstract</p> <p>Background</p> <p>Previous studies have documented lower breast cancer survival among women with lower socioeconomic status (SES) in the United States. In this study, I examined the extent to which socioeconomic disparity in breast cancer survival was explained by stage at diagnosis, treatment, race and rural/urban residence using the Surveillance, Epidemiology, and End Results (SEER) data.</p> <p>Methods</p> <p>Women diagnosed with breast cancer during 1998-2002 in the 13 SEER cancer registry areas were followed-up to the end of 2005. The association between an area-based measure of SES and cause-specific five-year survival was estimated using Cox regression models. Six models were used to assess the extent to which SES differences in survival were explained by clinical and demographical factors. The base model estimated the hazard ratio (HR) by SES only and then additional adjustments were made sequentially for: 1) age and year of diagnosis; 2) stage at diagnosis; 3) first course treatment; 4) race; and 5) rural/urban residence.</p> <p>Results</p> <p>An inverse association was found between SES and risk of dying from breast cancer (p < 0.0001). As area-level SES falls, HR rises (1.00 → 1.05 → 1.23 → 1.31) with the two lowest SES groups having statistically higher HRs. This SES differential completely disappeared after full adjustment for clinical and demographical factors (p = 0.20).</p> <p>Conclusion</p> <p>Stage at diagnosis, first course treatment and race explained most of the socioeconomic disparity in breast cancer survival. Targeted interventions to increase breast cancer screening and treatment coverage in patients with lower SES could reduce much of socioeconomic disparity.</p

Validating Operator Event Sequence Diagrams: The case of an automated vehicle to human driver handovers

Abstract: Predicting what drivers will do as vehicle control is handed over to them from automation is a relatively new challenge for the motor vehicle industry. Operator Event Sequence Diagrams (OESDs) offer a way of modeling the interactions between the driver and vehicle automation in the handover of control. In this paper, two studies are presented in which a range of handover strategies are tested. The anticipated driver strategies were modeled using OESDs to serve as predictions of driver behavior. Drivers were then observed in two separate studies: (1) using a Lower‐Fidelity (vehicle seat and controls) simulator and (2) using a Higher‐Fidelity (whole vehicle) simulator. Driver behavior during a takeover task was categorized according to the signal detection paradigm into hits, misses, false alarms, and correct rejections. The results showed that for all strategies in both sets of studies, the median criterion for validity was exceeded ( φ > 0.8), suggesting that OESDs made good predictions of driver behavior during the handover of the vehicle from automation to manual control

Evaluation of serum glycoprotein biomarker candidates for detection of esophageal adenocarcinoma and surveillance of Barrett’s esophagus

Esophageal adenocarcinoma (EAC) is thought to develop from asymptomatic Barrett’s esophagus (BE) with a low annual rate of conversion. Current endoscopy surveillance for BE patients is probably not cost-effective. Previously, we discovered serum glycoprotein biomarker candidates which could discriminate BE patients from EAC. Here, we aimed to validate candidate serum glycoprotein biomarkers in independent cohorts, and to develop a biomarker candidate panel for BE surveillance. Serum glycoprotein biomarker candidates were measured in 301 serum samples collected from Australia (4 states) and USA (1 clinic) using previously established lectin magnetic bead array (LeMBA) coupled multiple reaction monitoring mass spectrometry (MRM-MS) tier 3 assay. The area under receiver operating characteristic curve (AUROC) was calculated as a measure of discrimination, and multivariate recursive partitioning was used to formulate a multimarker panel for BE surveillance. Complement C9 (C9), gelsolin (GSN), serum paraoxonase/arylesterase 1 (PON1) and serum paraoxonase/lactonase 3 (PON3) were validated as diagnostic glycoprotein biomarkers in lectin pull-down samples for EAC across both cohorts. A panel of 10 serum glycoprotein biomarker candidates discriminated BE patients not requiring intervention [BE+/- low grade dysplasia] from those requiring intervention [BE with high grade dysplasia (BE-HGD) or EAC] with an AUROC value of 0.93. Tissue expression of C9 was found to be induced in BE, dysplastic BE and EAC. In longitudinal samples from subjects that have progressed towards EAC, levels of serum C9 were significantly (P\u3c0.05) increased with disease progression in EPHA (erythroagglutinin from Phaseolus vulgaris) and NPL (Narcissus pseudonarcissus lectin) pull-down samples. The results confirm alteration of complement pathway glycoproteins during BE-EAC pathogenesis. Further prospective clinical validation of the confirmed biomarker candidates in a large cohort is warranted, prior to development of a first-line BE surveillance blood test