Langevin dynamics encapsulate the microscopic and emergent macroscopic properties of midge swarms

In contrast with bird flocks, fish schools and animal herds, midge swarms maintain cohesion but do not process global order. High-speed imaging techniques are now revealing that these swarms have surprisingly properties. Here I show that simple models found on the Langevin equation are consistent with this wealth of recent observations. The models predict correctly that large accelerations, exceeding 10 g, will be common and they predict correctly the co-existence of core condensed phases surrounded by dilute vapour phases. The models also provide new insights into the influence of environmental conditions on swarm dynamics. They predict that correlations between midges increase the strength of the effective force binding the swarm together. This may explain why such correlations are absent in laboratory swarms but present in natural swarms which contend with the wind and other disturbances. Finally, the models predict that swarms have fluid-like macroscopic mechanical properties and will slosh rather than slide back-and-forth after being abruptly displaced. This prediction offers a promising avenue for future experimentation that goes beyond current quasi-static testing which has revealed solid-like responses

MSSM Baryogenesis and Electric Dipole Moments: An Update on the Phenomenology

We explore the implications of electroweak baryogenesis for future searches for permanent electric dipole moments in the context of the minimal supersymmetric extension of the Standard Model (MSSM). From a cosmological standpoint, we point out that regions of parameter space that over-produce relic lightest supersymmetric particles can be salvaged only by assuming a dilution of the particle relic density that makes it compatible with the dark matter density: this dilution must occur after dark matter freeze-out, which ordinarily takes place after electroweak baryogenesis, implying the same degree of dilution for the generated baryon number density as well. We expand on previous studies on the viable MSSM regions for baryogenesis, exploring for the first time an orthogonal slice of the relevant parameter space, namely the (tan\beta, m_A) plane, and the case of non-universal relative gaugino-higgsino CP violating phases. The main result of our study is that in all cases lower limits on the size of the electric dipole moments exist, and are typically on the same order, or above, the expected sensitivity of the next generation of experimental searches, implying that MSSM electroweak baryogenesis will be soon conclusively tested.Comment: 23 pages, 10 figures, matches version published in JHE

Metabolite Cross-Feeding Enhances Virulence in a Model Polymicrobial Infection

Microbes within polymicrobial infections often display synergistic interactions resulting in enhanced pathogenesis; however, the molecular mechanisms governing these interactions are not well understood. Development of model systems that allow detailed mechanistic studies of polymicrobial synergy is a critical step towards a comprehensive understanding of these infections in vivo. In this study, we used a model polymicrobial infection including the opportunistic pathogen Aggregatibacter actinomycetemcomitans and the commensal Streptococcus gordonii to examine the importance of metabolite cross-feeding for establishing co-culture infections. Our results reveal that co-culture with S. gordonii enhances the pathogenesis of A. actinomycetemcomitans in a murine abscess model of infection. Interestingly, the ability of A. actinomycetemcomitans to utilize L-lactate as an energy source is essential for these co-culture benefits. Surprisingly, inactivation of L-lactate catabolism had no impact on mono-culture growth in vitro and in vivo suggesting that A. actinomycetemcomitans L-lactate catabolism is only critical for establishing co-culture infections. These results demonstrate that metabolite cross-feeding is critical for A. actinomycetemcomitans to persist in a polymicrobial infection with S. gordonii supporting the idea that the metabolic properties of commensal bacteria alter the course of pathogenesis in polymicrobial communities

Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch

Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.Comment: 14 pages, 4 figure

Asian dust-storm activity dominated by Chinese dynasty changes since 2000 BP

The Asian monsoon (AM) played an important role in the dynastic history of China, yet it remains unknown whether AM-mediated shifts in Chinese societies affect earth surface processes to the point of exceeding natural variability. Here, we present a dust storm intensity record dating back to the first unified dynasty of China (the Qin Dynasty, 221–207 B.C.E.). Marked increases in dust storm activity coincided with unified dynasties with large populations during strong AM periods. By contrast, reduced dust storm activity corresponded to decreased population sizes and periods of civil unrest, which was co-eval with a weakened AM. The strengthened AM may have facilitated the development of Chinese civilizations, destabilizing the topsoil and thereby increasing the dust storm frequency. Beginning at least 2000 years ago, human activities might have started to overtake natural climatic variability as the dominant controls of dust storm activity in eastern China

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

A phase II study to determine the ability of gefitinib to reverse fluoropyrimidine resistance in metastatic colorectal cancer (the INFORM study)

There are data suggesting that inhibition of epidermal growth factor receptor (EGFR) tyrosine kinase signalling may reverse resistance to fluoropyrimidine treatment. To investigate this further, the INFORM study was an open-label, non-comparative phase II study of gefitinib (Iressa, ZD1839; AstraZeneca, Wilmington, DE, USA) 250 mg daily in combination with 5-fluorouracil (5-FU administered as an intravenous 400 mg m−2 bolus injection followed by 2800 mg m−2 infusion over 46 h and folinic acid administered as a 350 mg infusion over 2 h) every 2 weeks for up to 12 cycles in 24 patients with metastatic colorectal cancer refractory to previous fluoropyrimidine treatment. There were no objective responses. The stable disease rate was 37.5% (95% CI: 18.80, 59.41), median progression-free survival measured 116 days and overall survival was 226 days. Quality of life was unchanged compared to baseline values, and the commonest toxicities were diarrhoea, rash and fatigue with 7 out of 24 (29%) patients having a grade 3 or 4 toxicity. Gefitinib does not sensitise patients with fluoropyrimidine refractory metastatic colorectal cancer to 5-FU chemotherapy

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats

<p>Abstract</p> <p>Background</p> <p>Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes.</p> <p>Results</p> <p>CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats.</p> <p>Conclusion</p> <p>In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(<it>n</it>) in space and O(<it>nm</it>/<it>l</it>) in time.</p