Using error correction to determine the noise model

Quantum error correcting codes have been shown to have the ability of making quantum information resilient against noise. Here we show that we can use quantum error correcting codes as diagnostics to characterise noise. The experiment is based on a three-bit quantum error correcting code carried out on a three-qubit nuclear magnetic resonance (NMR) quantum information processor. Utilizing both engineered and natural noise, the degree of correlations present in the noise affecting a two-qubit subsystem was determined. We measured a correlation factor of c=0.5+/-0.2 using the error correction protocol, and c=0.3+/-0.2 using a standard NMR technique based on coherence pathway selection. Although the error correction method demands precise control, the results demonstrate that the required precision is achievable in the liquid-state NMR setting.Comment: 10 pages, 3 figures. Added discussion section, improved figure

Sex-Specific Growth and Reproductive Dynamics of Red Drum in the Northern Gulf of Mexico

The Red Drum Sciaenops ocellatus stock is heavily targeted in the Gulf of Mexico (GOM) by recreational fishers and supports a small commercial fishery in Mississippi. Despite their popularity, little recent work has been done to describe their life history. In this work, we describe sex‐specific growth and reproductive dynamics of Red Drum collected from the northern GOM from September 2016 through October 2017. We evaluated seven candidate growth models and found that the three‐parameter von Bertalanffy growth function (VBGF) was the best candidate length‐at‐age model. No significant difference in growth between sexes was observed with the three‐parameter VBGF, despite the female‐specific curve having a larger mean asymptotic length than the male‐specific curve. All seven candidate growth models predicted similar mean length‐at‐age estimates, and four of them exhibited significant differences in sex‐specific mean length at age, with females reaching a larger length at age than males after age 5. There was no significant difference between the sex‐specific weight‐at‐length relationships. Red Drum are batch spawners that spawn in northern GOM coastal waters during August and September. We estimated 3.7 d between spawns and 10.5 spawning events per female in 2017. Nearly 20% of fish collected during the spawning season were sexually mature but reproductively inactive, indicating the possibility of skipped spawning. The age at 50% maturity was around 3 years (length at 50% maturity = 670 mm TL) in both sexes, but fish were not spawning capable until age 4.5 (703 mm TL) in males and age 5.8 (840 mm TL) in females. Furthermore, elevated gonadosomatic indices were not observed until around age 5–6. The updated life history information presented in this work helps to address current data limitations and provides critical information for future assessments of Red Drum stocks in the northern GOM

Coupling of a Core Post-Translational Pacemaker to a Slave Transcription/Translation Feedback Loop in a Circadian System

Analysis of the cyanobacterial circadian biological clock reveals a complex interdependence between a transcription/translation feedback loop and a biochemical oscillator

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences [13–16]. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org])

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators

To characterize the behavior and robustness of cellular circuits with many unknown parameters is a major challenge for systems biology. Its difficulty rises exponentially with the number of circuit components. We here propose a novel analysis method to meet this challenge. Our method identifies the region of a high-dimensional parameter space where a circuit displays an experimentally observed behavior. It does so via a Monte Carlo approach guided by principal component analysis, in order to allow efficient sampling of this space. This ‘global’ analysis is then supplemented by a ‘local’ analysis, in which circuit robustness is determined for each of the thousands of parameter sets sampled in the global analysis. We apply this method to two prominent, recent models of the cyanobacterial circadian oscillator, an autocatalytic model, and a model centered on consecutive phosphorylation at two sites of the KaiC protein, a key circadian regulator. For these models, we find that the two-sites architecture is much more robust than the autocatalytic one, both globally and locally, based on five different quantifiers of robustness, including robustness to parameter perturbations and to molecular noise. Our ‘glocal’ combination of global and local analyses can also identify key causes of high or low robustness. In doing so, our approach helps to unravel the architectural origin of robust circuit behavior. Complementarily, identifying fragile aspects of system behavior can aid in designing perturbation experiments that may discriminate between competing mechanisms and different parameter sets

Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach

CaMdr1p is a multidrug MFS transporter of pathogenic Candida albicans. An over-expression of the gene encoding this protein is linked to clinically encountered azole resistance. In-depth knowledge of the structure and function of CaMdr1p is necessary for an effective design of modulators or inhibitors of this efflux transporter. Towards this goal, in this study, we have employed a membrane environment based computational approach to predict the functionally critical residues of CaMdr1p. For this, information theoretic scores which are variants of Relative Entropy (Modified Relative Entropy REM) were calculated from Multiple Sequence Alignment (MSA) by separately considering distinct physico-chemical properties of transmembrane (TM) and inter-TM regions. The residues of CaMdr1p with high REM which were predicted to be significantly important were subjected to site-directed mutational analysis. Interestingly, heterologous host Saccharomyces cerevisiae, over-expressing these mutant variants of CaMdr1p wherein these high REM residues were replaced by either alanine or leucine, demonstrated increased susceptibility to tested drugs. The hypersensitivity to drugs was supported by abrogated substrate efflux mediated by mutant variant proteins and was not attributed to their poor expression or surface localization. Additionally, by employing a distance plot from a 3D deduced model of CaMdr1p, we could also predict the role of these functionally critical residues in maintaining apparent inter-helical interactions to provide the desired fold for the proper functioning of CaMdr1p. Residues predicted to be critical for function across the family were also found to be vital from other previously published studies, implying its wider application to other membrane protein families

Integrating an internet-mediated walking program into family medicine clinical practice: a pilot feasibility study

<p>Abstract</p> <p>Background</p> <p>Regular participation in physical activity can prevent many chronic health conditions. Computerized self-management programs are effective clinical tools to support patient participation in physical activity. This pilot study sought to develop and evaluate an online interface for primary care providers to refer patients to an Internet-mediated walking program called Stepping Up to Health (SUH) and to monitor participant progress in the program.</p> <p>Methods</p> <p>In Phase I of the study, we recruited six pairs of physicians and medical assistants from two family practice clinics to assist with the design of a clinical interface. During Phase II, providers used the developed interface to refer patients to a six-week pilot intervention. Provider perspectives were assessed regarding the feasibility of integrating the program into routine care. Assessment tools included quantitative and qualitative data gathered from semi-structured interviews, surveys, and online usage logs.</p> <p>Results</p> <p>In Phase I, 13 providers used SUH and participated in two interviews. Providers emphasized the need for alerts flagging patients who were not doing well and the ability to review participant progress. Additionally, providers asked for summary views of data across all enrolled clinic patients as well as advertising materials for intervention recruitment. In response to this input, an interface was developed containing three pages: 1) a recruitment page, 2) a summary page, and 3) a detailed patient page. In Phase II, providers used the interface to refer 139 patients to SUH and 37 (27%) enrolled in the intervention. Providers rarely used the interface to monitor enrolled patients. Barriers to regular use of the intervention included lack of integration with the medical record system, competing priorities, patient disinterest, and physician unease with exercise referrals. Intention-to-treat analyses showed that patients increased walking by an average of 1493 steps/day from pre- to post-intervention (<it>t </it>= (36) = 4.13, <it>p </it>< 0.01).</p> <p>Conclusions</p> <p>Providers successfully referred patients using the SUH provider interface, but were less willing to monitor patient compliance in the program. Patients who completed the program significantly increased their step counts. Future research is needed to test the effectiveness of integrating SUH with clinical information systems over a longer evaluation period.</p