Observation of anomalous spin-state segregation in a trapped ultra-cold vapor

We observe counter-intuitive spin segregation in an inhomogeneous sample of ultra-cold, non-condensed Rubidium atoms in a magnetic trap. We use spatially selective microwave spectroscopy to verify a model that accounts for the differential forces on two internal spin states. In any simple understanding of the cloud dynamics, the forces are far too small to account for the dramatic transient spin polarizations observed. The underlying mechanism remains to be elucidated.Comment: 5 pages, 3 figure

Internal state conversion in ultracold gases

We consider an ultracold gas of (non-condensed) bosons or fermions with two internal states, and study the effect of a gradient of the transition frequency between these states. When a $\pi/2$ RF pulse is applied to the sample, exchange effects during collisions transfer the atoms into internal states which depend on the direction of their velocity. This results, after a short time, in a spatial separation between the two states. A kinetic equation is solved analytically and numerically; the results agree well with the recent observations of Lewandowski et al.Comment: Accepted version, to appear in PR

Calculation of NMR Properties of Solitons in Superfluid 3He-A

Superfluid 3He-A has domain-wall-like structures, which are called solitons. We calculate numerically the structure of a splay soliton. We study the effect of solitons on the nuclear-magnetic-resonance spectrum by calculating the frequency shifts and the amplitudes of the soliton peaks for both longitudinal and transverse oscillations of magnetization. The effect of dissipation caused by normal-superfluid conversion and spin diffusion is calculated. The calculations are in good agreement with experiments, except a problem in the transverse resonance frequency of the splay soliton or in magnetic-field dependence of reduced resonance frequencies.Comment: 15 pages, 10 figures, updated to the published versio

On dynamic network entropy in cancer

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level insights into disease mechanisms and ultimately for developing improved therapies. By integrating gene expression data with a protein interaction network to induce a stochastic dynamics on the network, we here demonstrate that cancer cells are characterised by an increase in the dynamic network entropy, compared to cells of normal physiology. Using a fundamental relation between the macroscopic resilience of a dynamical system and the uncertainty (entropy) in the underlying microscopic processes, we argue that cancer cells will be more robust to random gene perturbations. In addition, we formally demonstrate that gene expression differences between normal and cancer tissue are anticorrelated with local dynamic entropy changes, thus providing a systemic link between gene expression changes at the nodes and their local network dynamics. In particular, we also find that genes which drive cell-proliferation in cancer cells and which often encode oncogenes are associated with reductions in the dynamic network entropy. In summary, our results support the view that the observed increased robustness of cancer cells to perturbation and therapy may be due to an increase in the dynamic network entropy that allows cells to adapt to the new cellular stresses. Conversely, genes that exhibit local flux entropy decreases in cancer may render cancer cells more susceptible to targeted intervention and may therefore represent promising drug targets.Comment: 10 pages, 3 figures, 4 tables. Submitte

Text mining for the biocuration workflow

Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community

Forecast for HEAT on Dome A, Antarctica: the High Elevation Antarctic Terahertz Telescope

We have proposed to develop a prototype 0.5-meter far-infrared telescope and heterodyne receiver/spectrometer system for fully-automated remote operation at the summit of Dome A, the highest point on the Antarctic plateau. The unparalleled stability, exceptional dryness, low wind and extreme cold make Dome A a ground-based site without equal for astronomy at infrared and submillimeter wavelengths. HEAT, the High Elevation Antarctic Terahertz Telescope, will operate in the atmospheric windows between 150 and 400 microns, in which the most crucial astrophysical spectral diagnostics of the formation of galaxies, stars, planets, and life are found. At these wavelengths, HEAT will have high aperture efficiency and excellent atmospheric transmission most of the year. The proposed superheterodyne receiver system will be comprised of 0.8, 1.4 and 1.9 THz channels which will observe the pivotal J=7-6 line of CO, the J=2-1 line of atomic carbon, and the far-infrared fine structure lines of N+ and C+, the brightest emission lines in the entire Milky Way Galaxy. When combined with the HEAT telescope, the receiver system represents a uniquely powerful instrument for reconstructing the history of star formation in our Galaxy, with application to the distant Universe. The receiver system itself serves as a valuable testbed for heterodyne Terahertz components, using leading-edge mixer, local oscillator, low-noise amplifier, cryogenic, and digital signal processing technologies that will play essential roles in future Terahertz observatories. The proposed study will pave the way for future astronomical investigations from Dome A

THE ROLE OF INTERDEPENDENCE IN THE MICRO-FOUNDATIONS OF ORGANIZATION DESIGN: TASK, GOAL, AND KNOWLEDGE INTERDEPENDENCE

Interdependence is a core concept in organization design, yet one that has remained consistently understudied. Current notions of interdependence remain rooted in seminal works, produced at a time when managers’ near-perfect understanding of the task at hand drove the organization design process. In this context, task interdependence was rightly assumed to be exogenously determined by characteristics of the work and the technology. We no longer live in that world, yet our view of interdependence has remained exceedingly task-centric and our treatment of interdependence overly deterministic. As organizations face increasingly unpredictable workstreams and workers co-design the organization alongside managers, our field requires a more comprehensive toolbox that incorporates aspects of agent-based interdependence. In this paper, we synthesize research in organization design, organizational behavior, and other related literatures to examine three types of interdependence that characterize organizations’ workflows: task, goal, and knowledge interdependence. We offer clear definitions for each construct, analyze how each arises endogenously in the design process, explore their interrelations, and pose questions to guide future research

Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation

How cells coordinate the immune system activities is important for potentially life-saving organ or stem cell transplantations. Polymorphic immunoregulatory genes, many of them located in the human major histocompatibility complex, impact the process and assure the proper execution of tolerance-versus-activity mechanisms. In haematopoietic stem cell transplantation, on the basis of fully human leukocyte antigen (HLA)-matched donor–recipient pairs, adverse effects like graft versus leukaemia and graft versus host are observed and difficult to handle. So far, high-resolution HLA typing was performed with Sanger sequencing, but for methodological reasons information on additional immunocompetent major histocompatibility complex loci has not been revealed. Now, we have used microarray sequence capture and targeted enrichment combined with next generation pyrosequencing for 3.5 million base pair human major histocompatibility complex resequencing in a clinical transplant setting and describe 3025 variant single nucleotide polymorphisms, insertions and deletions among recipient and donor in a single sequencing experiment. Taken together, the presented data show that sequence capture and massively parallel pyrosequencing can be used as a new tool for risk assessment in the setting of allogeneic stem cell transplantation