Stability of the nonlinear dynamics of an optically injected VCSEL

Automated protocols have been developed to characterize time series data in terms of stability. These techniques are applied to the output power time series of an optically injected vertical cavity surface emitting laser (VCSEL) subject to varying injection strength and optical frequency detuning between master and slave lasers. Dynamic maps, generated from high resolution, computer controlled experiments, identify regions of dynamic instability in the parameter space. © 2012 Optical Society of America

Reconstructing 7000 years of North Atlantic hurricane variability using deep-sea sediment cores from the western Great Bahama Bank

Author Posting. © American Geophysical Union, 2013. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 28 (2013): 31–41, doi:10.1002/palo.20012.Available overwash records from coastal barrier systems document significant variability in North Atlantic hurricane activity during the late Holocene. The same climate forcings that may have controlled cyclone activity over this interval (e.g., the West African Monsoon, El Niño–Southern Oscillation (ENSO)) show abrupt changes around 6000 yrs B.P., but most coastal sedimentary records do not span this time period. Establishing longer records is essential for understanding mid-Holocene patterns of storminess and their climatic drivers, which will lead to better forecasting of how climate change over the next century may affect tropical cyclone frequency and intensity. Storms are thought to be an important mechanism for transporting coarse sediment from shallow carbonate platforms to the deep-sea, and bank-edge sediments may offer an unexplored archive of long-term hurricane activity. Here, we develop this new approach, reconstructing more than 7000 years of North Atlantic hurricane variability using coarse-grained deposits in sediment cores from the leeward margin of the Great Bahama Bank. High energy event layers within the resulting archive are (1) broadly correlated throughout an offbank transect of multi-cores, (2) closely matched with historic hurricane events, and (3) synchronous with previous intervals of heightened North Atlantic hurricane activity in overwash reconstructions from Puerto Rico and elsewhere in the Bahamas. Lower storm frequency prior to 4400 yrs B.P. in our records suggests that precession and increased NH summer insolation may have greatly limited hurricane potential intensity, outweighing weakened ENSO and a stronger West African Monsoon—factors thought to be favorable for hurricane development.This research was supported by awards from the Division of Ocean Sciences and the Division of Atmospheric and Geospace Sciences of the National Science Foundation to William B. Curry and an NSERC Post-Doctoral Fellowship to Peter van Hengstum.2013-09-1

Seismic evidence of glacial-age river incision into the Tahaa barrier reef, French Polynesia

This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 380 (2016): 284–289, doi:10.1016/j.margeo.2016.04.008.Rivers have long been recognized for their ability to shape reef-bound volcanic islands. On the time-scale of glacial–interglacial sea-level cycles, fluvial incision of exposed barrier reef lagoons may compete with constructional coral growth to shape the coastal geomorphology of ocean islands. However, overprinting of Pleistocene landscapes by Holocene erosion or sedimentation has largely obscured the role lowstand river incision may have played in developing the deep lagoons typical of modern barrier reefs. Here we use high-resolution seismic imagery and core stratigraphy to examine how erosion and/or deposition by upland drainage networks has shaped coastal morphology on Tahaa, a barrier reef-bound island located along the Society Islands hotspot chain in French Polynesia. At Tahaa, we find that many channels, incised into the lagoon floor during Pleistocene sea-level lowstands, are located near the mouths of upstream terrestrial drainages. Steeper antecedent topography appears to have enhanced lowstand fluvial erosion along Tahaa's southwestern coast and maintained a deep pass. During highstands, upland drainages appear to contribute little sediment to refilling accommodation space in the lagoon. Rather, the flushing of fine carbonate sediment out of incised fluvial channels by storms and currents appears to have limited lagoonal infilling and further reinforced development of deep barrier reef lagoons during periods of highstand submersion.This project was supported by a Jackson School Distinguished Postdoctoral Fellowship to Michael Toomey and the WHOI Coastal Ocean Institute and Ocean and Climate Change Institute

Low-Temperature Physics

Contains reports on four research projects

Genomes2Drugs: Identifies Target Proteins and Lead Drugs from Proteome Data

Background: Genome sequencing and bioinformatics have provided the full hypothetical proteome of many pathogenic organisms. Advances in microarray and mass spectrometry have also yielded large output datasets of possible target proteins/genes. However, the challenge remains to identify new targets for drug discovery from this wealth of information. Further analysis includes bioinformatics and/or molecular biology tools to validate the findings. This is time consuming and expensive, and could fail to yield novel drugs if protein purification and crystallography is impossible. To pre-empt this, a researcher may want to rapidly filter the output datasets for proteins that show good homology to proteins that have already been structurally characterised or proteins that are already targets for known drugs. Critically, those researchers developing novel antibiotics need to select out the proteins that show close homology to any human proteins, as future inhibitors are likely to cross-react with the host protein, causing off-target toxicity effects later in clinical trials. Methodology/Principal Findings: To solve many of these issues, we have developed a free online resource called Genomes2Drugs which ranks sequences to identify proteins that are (i) homologous to previously crystallized proteins or (ii) targets of known drugs, but are (iii) not homologous to human proteins. When tested using the Plasmodium falciparum malarial genome the program correctly enriched the ranked list of proteins with known drug target proteins. Conclusions/Significance: Genomes2Drugs rapidly identifies proteins that are likely to succeed in drug discovery pipelines

Understanding Face and Shame: A Servant-Leadership and Face Management Model

Clergy can have a negative impact on churches and other individuals when they knowingly or unknowingly attempt to save face, that is, try to protect their standing or reputation. The desire to gain face and the fear of losing face and feeling ashamed will likely permeate clergy’s decision-making processes without even being noticed. This study explores the essence of face and face management and the relationship between face management and two characteristics of servant-leadership—awareness and healing—in both Chinese and American churches through the methodology of hermeneutic phenomenology. Prior to this study, to my knowledge, no hermeneutic phenomenological research of face management has been conducted in a church setting. Through a review of the literature, four areas are explored: face and shame, face management, servant-leadership, and face, shame, and face management within the church. This study obtained approval from the Institutional Review Board and informed consent from the participants. Three Chinese and three American Christian ministers were chosen to complete a question sheet and participate in two semi-structured interview sessions. A first cycle of open coding and second cycle of pattern coding were used during data analysis. Face experiences are discussed in light of eight major themes: body, triggers, becoming, face concepts, strategies, emotions, servant-leadership, and the church. Findings from the study help build a servant-leadership and face management model, which can offer an anchored approach for clergy and pastoral counselors to address face and shame and to develop therapeutic interventions

Timing analysis for 20 millisecond pulsars in the Parkes Pulsar Timing Array

We present timing models for 20 millisecond pulsars in the Parkes Pulsar Timing Array. The precision of the parameter measurements in these models has been improved over earlier results by using longer data sets and modelling the non-stationary noise. We describe a new noise modelling procedure and demonstrate its effectiveness using simulated data. Our methodology includes the addition of annual dispersion measure (DM) variations to the timing models of some pulsars. We present the first significant parallax measurements for PSRs J1024-0719, J1045-4509, J1600-3053, J1603-7202, and J1730-2304, as well as the first significant measurements of some post-Keplerian orbital parameters in six binary pulsars, caused by kinematic effects. Improved Shapiro delay measurements have resulted in much improved pulsar mass measurements, particularly for PSRs J0437-4715 and J1909-3744 with $M_p=1.44\pm0.07$ $M_\odot$ and $M_p=1.47\pm0.03$ $M_\odot$ respectively. The improved orbital period-derivative measurement for PSR J0437-4715 results in a derived distance measurement at the 0.16% level of precision, $D=156.79\pm0.25$ pc, one of the most fractionally precise distance measurements of any star to date.Comment: 21 pages, 5 figures, 7 tables. Accepted for publication in MNRA

TIRSPEC : TIFR Near Infrared Spectrometer and Imager

We describe the TIFR Near Infrared Spectrometer and Imager (TIRSPEC) designed and built in collaboration with M/s. Mauna Kea Infrared LLC, Hawaii, USA, now in operation on the side port of the 2-m Himalayan Chandra Telescope (HCT), Hanle (Ladakh), India at an altitude of 4500 meters above mean sea level. The TIRSPEC provides for various modes of operation which include photometry with broad and narrow band filters, spectrometry in single order mode with long slits of 300" length and different widths, with order sorter filters in the Y, J, H and K bands and a grism as the dispersing element as well as a cross dispersed mode to give a coverage of 1.0 to 2.5 microns at a resolving power R of ~1200. The TIRSPEC uses a Teledyne 1024 x 1024 pixel Hawaii-1 PACE array detector with a cutoff wavelength of 2.5 microns and on HCT, provides a field of view of 307" x 307" with a plate scale of 0.3"/pixel. The TIRSPEC was successfully commissioned in June 2013 and the subsequent characterization and astronomical observations are presented here. The TIRSPEC has been made available to the worldwide astronomical community for science observations from May 2014.Comment: 20 pages, 21 figures, 2 tables. Accepted for publication in Journal of Astronomical Instrumentatio

Establishing Professional Intercultural Relations: Chinese Perceptions of Behavioural Success in a Sino-American Exchange Visit

This article examines the ways in which professionals from different countries handle first encounters when they wish to initiate and establish business/professional relations. The majority of research on business relations in intercultural contexts has so far focused on misunderstandings, face threats, and conflict. There has been comparatively little research into the initiation and establishment of relations from a positive perspective. This article addresses this lacuna by analysing how Chinese delegates built positive relations with American counterparts on a visit to the USA. Drawing on insights from the analysis, it proposes a conceptual framework for future research in this area

Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome

peer-reviewedBackground Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary intervention with high-CLA beef, a range of plasma markers indicated a marked improvement in the metabolic health of genetically obese mice. Tissue transcriptomic profiles indicated that the effects were most dramatic in liver (1270 genes significantly changed; p < 0.05), followed by muscle (601 genes) and adipose (16 genes). Results from modified GSEA showed that the high-CLA beef diet affected diverse biological processes across the three tissues, and that the majority of pathway changes reached significance only with the bi-directional test. Combining the liver tissue microarray results with plasma marker data revealed 110 CLA-sensitive genes showing strong canonical correlation with one or more plasma markers of metabolic health, and 9 significantly overrepresented pathways among this set; each of these pathways was also significantly changed by the high-CLA diet. Closer inspection of two of these pathways - selenoamino acid metabolism and steroid biosynthesis - illustrated clear diet-sensitive changes in constituent genes, as well as strong correlations between gene expression and plasma markers of metabolic syndrome independent of the dietary effect. Conclusion Bi-directional gene set enrichment analysis more accurately reflects dynamic regulatory behaviour in biochemical pathways, and as such highlighted biologically relevant changes that were not detected using a traditional approach. In such cases where transcriptomic response to treatment is exceptionally large, canonical correlation analysis in conjunction with Fisher's exact test highlights the subset of pathways showing strongest correlation with the clinical markers of interest. In this case, we have identified selenoamino acid metabolism and steroid biosynthesis as key pathways mediating the observed relationship between metabolic health and high-CLA beef. These results indicate that this type of analysis has the potential to generate novel transcriptome-based biomarkers of disease.Department of Agriculture and Food, Ireland - Food Institutional Research Measure (project no. 5254); IRCSET postgraduate scholarship scheme (MJM); Science Foundation Ireland Principal Investigator Programme (HMR) Programme