EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)

BACKGROUND: Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. RESULTS: The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site through the quick link 'Browse Records by 3D Structure.' CONCLUSION: The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required

Towards Communication-Efficient Quantum Oblivious Key Distribution

Oblivious Transfer, a fundamental problem in the field of secure multi-party computation is defined as follows: A database DB of N bits held by Bob is queried by a user Alice who is interested in the bit DB_b in such a way that (1) Alice learns DB_b and only DB_b and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi et al. [Phys. Rev. A, 83(2), 022301, Feb 2011] proposed a protocol for Oblivious Transfer using well known QKD techniques to establish an Oblivious Key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like impossibility of perfectly distinguishing non-orthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of SARG04). However, their Quantum Oblivious Key Distribution (QOKD) protocol requires a communication complexity of O(N log N). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.Comment: 7 page

Horse Welfare During Equine Chorionic Gonadotropin (eCG) Production

Equine chorionic gonadotropin or eCG is an important hormone produced by the placenta of pregnant mares and extracted from the blood of these same mares. This hormone is commonly used to enhance reproduction of pigs, dairy cows, sheep, beef cows, and goats. There are currently no alternative sources of this hormone. Horse welfare problems may arise if too much blood is collected at one time or during repeated collections or if the mares are not managed well. In some countries, mares are aborted several months into the pregnancy to improve efficiency since this permits them to become pregnant a second time in one year. We discuss approaches to protect the welfare of pregnant mares kept for eCG production. Collection of blood from pregnant mares for extraction of equine chorionic gonadotropin (eCG) is a critical but relatively unknown and poorly regulated practice in the countries in which it occurs. Equine chorionic gonadotropin is a hormone that is widely used to enhance reproductive performance and management of dairy and beef cattle, sheep, goats, and pigs kept under intensive housing systems. eCG is extracted from the blood of brood mares between days 40-120 of gestation. Although alternatives have been sought, there is currently no efficacious replacement, natural or synthetic, for eCG. Recently, several animal welfare organizations have voiced concerns over the condition and treatment of pregnant mares kept for eCG production in some countries. Animal welfare issues may arise if mares are bled too frequently or if too much blood is collected at any time. In addition, these mares tend to be managed extensively on pastures with minimal veterinary oversight and they may be poorly desensitized and habituated to handling and other practices. This can lead to serious injuries and even death when mares are brought in for bleeding. This paper reviews the process of blood collection for eCG extraction and provides recommendations for ensuring mare welfare

AO 0235+164 and Surrounding Field: Surprising HST Results

Results obtained with the Hubble Space Telescope on the highly variable radio, x-ray, and gamma-ray emitting QSO (or BL Lac object) AO 0235 + 164 are presented and analyzed. WFPC2 images were obtained in 1994 June, when AO 0235 + 164 was bright (m approx. 17), and the results are described in Sec. 3. After subtraction of the PSF of the QSO, hereafter called AO following the nomenclature of Yanny et al. (1989), the companion object named A, 2 sec south of AO, is discovered not to be an elliptical galaxy as hypothesized earlier, but to be an AGN object, with a central UV-bright point-source nucleus and faint surrounding nebulosity extending to AO. The second companion object 1.3 sec east of AO discovered by Yanny et al. (1989) and named object Al, appears more like a normal spiral galaxy. We have measured the positions, luminosities, and colors of some 30 faint objects in the field around AO 0235 + 16; most are extended and may be star-forming galaxies in a loose group or cluster. Our most surprising result of the HST observations comes from FOS spectra obtained in 1995 July, discussed in Sec. 4. Because of a positioning error of the telescope and AO's faintness at that time (m approx. 20), object A was observed instead of the intended target AO. Serendipitously, we discovered A to have broad deep BALQSO-type absorptions of C IV, Si IV, N V shortward of broad emissions. A is thus ejecting high velocity, highly ionized gas into the surrounding IGM. We discuss in Sec. 5 the relationship of the objects in the central 10 sec X 1O sec region around AO, where redshifts z(sub e) = 0.94, z(sub a) = 0.524, 0.851 in AO, (sub e) = 0.524 and Z(sub BAL)=0.511 in A, are found. We hypothesize that some of the 30 faint objects in the 77 sec. x 77 sec. field may be part of a large star-forming region at z approx. 0.5, as suggested for a few objects by Yanny et al. (1989). The proximity of two highly active extragalactic objects, AO 0235+164 and its AGN companion A, is remarkable and one of the authors (EMB) suggests it may require consideration of a non-cosmological component of redshift in AO 0235+164

Sonic crystal lenses that obey Lensmaker's formula

This paper presents a theoretical study of the phenomenon of acoustic imaging by sonic crystals, which are made of two-dimensional regular arrays of rigid cylinders placed in parallel in air. The scattering of acoustic waves is computed using the standard multiple scattering theory, and the band structures are computed by the plane-wave expansion method. It is shown that properly arranged arrays not only can behave as acoustic lenses, but also the focusing effect can be well described by Lensmaker's formula. Possible applications are also discussed.Comment: 4 pages, 5 figure

Paleomagnetic Constraints From South Georgia On The Tectonic Reconstruction Of The Early Cretaceous Rocas Verdes Marginal Basin System Of Southernmost South America

South Georgia exists as a microcontinent along the North Scotia Ridge ∼1,700 km east of Cape Horn. The tectonostratigraphic units of South Georgia have long been correlated with those of the Fuegian Andes of southernmost South America. Accordingly, South Georgia has been regarded as a continuation of the Late Jurassic–Early Cretaceous Rocas Verdes marginal basin system, formerly situated south of Burdwood Bank and east of Cape Horn. To test this, paleomagnetic analysis of samples from the Larsen Harbour Complex, Drygalski Fjord Complex, and Annenkov Island Formation of South Georgia showed that 21 sites yield a mean direction of D = 328.5°, I = −62.1° (a95 = 3.5°) and a paleomagnetic pole at 068.2°E, 67.2°N, A95 = 4.7°. The consistency of directions and strong polarity bias, plus indications of a negative differential tilt test, point to a secondary magnetization acquired in the Late Cretaceous. Comparison of predicted versus observed directions for South Georgia relative to stable South America indicate 27.2 ± 11.2° of counter-clockwise rotation (and 10.5° ± 4.5° of northward tilting) since the acquisition of magnetization. These results are consistent with paleomagnetic studies from the Fuegian Andes and support a paleoposition of the South Georgia microcontinent south of Burdwood Bank as strongly indicated by the geologic evidence. Partitioning this rotation between oroclinal bending during the Rocas Verdes basin collapse in the Late Cretaceous and left-lateral translation along the North Scotia Ridge is not possible on paleomagnetic grounds, but the co-linearity of Andean structures between the restored microcontinent and Tierra del Fuego indicates the former

Being Healthy: a Grounded Theory Study of Help Seeking Behaviour among Chinese Elders living in the UK

The health of older people is a priority in many countries as the world’s population ages. Attitudes towards help seeking behaviours in older people remain a largely unexplored field of research. This is particularly true for older minority groups where the place that they have migrated to presents both cultural and structural challenges. The UK, like other countries,has an increasingly aging Chinese population about who relatively little is known. This study used a qualitative grounded theory design following the approach of Glaser (1978). Qualitative data were collected using semi-structured interviews with 33 Chinese elders who were aged between 60 and 84, using purposive and theoretical sampling approaches. Data were analysed using the constant comparative method until data saturation occurred and a substantive theory was generated. ‘Being healthy’ (the core category) with four interrelated categories: self-management, normalizing/minimizing, access to health services, and being cured form the theory. The theory was generated around the core explanations provided by participants and Chinese elders’ concerns about health issues they face in their daily life. We also present data about how they direct their health-related activities towards meeting their physical and psychological goals of being healthy. Their differential understanding of diseases and a lack of information about health services were potent predictors of non�help seeking and ‘self’ rather than medical management of their illnesses. This study highlights the need for intervention and health support for Chinese elders

LBQS 0103-2753: A 0.3 Arcsec Binary Quasar

Imaging and spectroscopy with HST show that LBQS 0103-2753 (V = 17.8, z = 0.848) is a binary quasar with a separation of 0.3 arcsec or 2.3 kpc. This is by far the smallest separation binary quasar reported to date. The two components have very different spectra, including the presence of strong broad absorption lines (BALs) in component A only. The emission-line redshifts, based on the broad high ionization C IV lines, are z_A = 0.834 and z_B = 0.858; their difference is 3900 km/s in velocity units. The broad C IV lines, however, are probably not a good indicator of systemic redshift; and LBQS 0103-2753 A and B could have a much smaller systemic redshift difference, like the other known binary quasars. If the systemic redshift difference is small, then LBQS 0103-2753 would most likely be a galaxy merger that has led to a binary supermassive black hole. There is now one known 0.3 arcsec binary among roughly 500 QSOs that have been observed in a way that would reveal such a close binary. This suggests that QSO activity is substantially more likely for black hole binaries at spacings ~2 kpc than at ~15 to 60 kpc. Between 1987 and 1998, the observed Mg II BAL disappeared.Comment: 12 pages LATEX with 3 EPS figures; uses aaspp4.sty. Accepted for publication in The Astrophysical Journal Letters, volume 550 (2001 March 20