PRECIS: Protein reports engineered from concise information in SWISS-PROT

Motivation: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords. Availability: The software is accessible online at: http://www.bioinf.man.ac.uk/cgi-bin/dbbrowser/precis/blast_precis.cg

Spanish question answering evaluation

This paper reports the most significant issues related to the launching of a Monolingual Spanish Question Answering evaluation track at the Cross Language Evaluation Forum (CLEF 2003). It introduces some questions about multilingualism and describes the methodology for test suite production, task, judgment of answers as well as the results obtained by the participant systems

Intersectional Value? A Pilot Study Exploring Educational Outcomes for African American Women in Historically Black Sororities Versus Non-Historically Black Sororities

The purpose of this pilot study was to initially explore if there is value added in terms of educational outcomes for Black women involved in historically Black sororities by comparing them to Black women involved in non-historically Black sororities, given the racial-gender support historically Black sororities offer. Main findings suggest Black women involved in historically Black sororities were more socially involved than Black women involved in non-historically Black sororities. The article closes with implications for practice and future research

Resources and student achievement – evidence from a Swedish policy reform

This paper utilizes a policy change to estimate the effect of teacher density on student performance. We find that an increase in teacher density has a positive effect on student achievement. The baseline estimate – obtained by using the grade point average as the outcome variable – implies that resource increases corresponding to the class-size reduction in the STAR-experiment (i.e., a reduction of 7 students) improves performance by 2.6 percentile ranks (or 0.08 standard deviations). When we use test score data for men, potentially a more objective measure of student performance, the effect of resources appears to be twice the size of the baseline estimate.Student performance; teacher/student ratio; policy reform; differences-in-differences

The Beagle landing site in Isidis Planitia

The Mars probe Beagle 2 will land in Isidis Planitia. This region satisfies the engineering constraints and has evidence for particularly volatile-rich subsoil. Isidis provides a suitable place for the lander to search for H2O and organic matter

New, efficient and robust, fiber-based quantum key distribution schemes

We present a new fiber based quantum key distribution (QKD) scheme which can be regarded as a modification of an idea proposed by Inoue, Waks and Yamamoto (IWY) [1]. The scheme described here uses a single phase modulator and two differential delay elements in series at the transmitter that form an interferometer when combined with a third differential delay element at the receiver. The protocol is characterized by a high efficiency, reduced exposure to an attack by an eavesdropper, and higher sensitivity to such an attack when compared to other QKD schemes. For example, the efficiency with which transmitted data contribute to the private key is 3/4 compared with 1/4 for BB84 [2]. Moreover, an eavesdropper can aquire a maximum of 1/3 of the key which leads to an error probability in the private key of 1/3. This can be compared to 1/2 and 1/4 for these same parameters in both BB84 and IWY. The combination of these considerations should lead to increased range and key distribution rate over present fiber-based QKD schemes.Comment: 4 pages, 5 figures, 1 equatio

Soil conductivity study and implications for fish and farming compatibility in the Swinomish agricultural area

The Swinomish agricultural area, along the Swinomish Channel, is part of the Skagit River Delta, a major agrarian region in Puget Sound. Historically a complex system of tidal channels serving as salmon habitat, the tidelands have since been diked and drained. In 2005, the Swinomish Indian Tribal Community (SITC) began restoration to demonstrate compatibility of fish habitat and agriculture. Muted tidal regulators (MTRs) operated to optimize tidal inundation and fish passage, replaced traditional tidegates, and prompted a study to evaluate soil conductivity impacts on agriculture. Objectives included electromagnetic (EM) surveying of soil conductivity, qualitatively assessing EM results utilizing two additional methods, and assessing local crop suitability and restoration effectiveness for fish habitat and agriculture compatibility. All methods showed low conductivity throughout the majority of the area with isolated elevated levels adjacent to drainage ditches, the main Channel dike, and in low-lying depressional areas. Designed for periodic inundation, a restoration area yielded some of the highest conductivity levels. Using conversion formulas applicable to each conductivity measurement method, conductivity values were converted to salinity classes to evaluate potential adverse crop effects. The areas described above ranged from primarily ‘slightly saline’ and ‘moderately saline’ (many crop yields restricted), to ‘strongly saline’, with marginal ‘very strongly saline’ areas along the main dike and in the restoration area. However, the vast majority of the agricultural area could be categorized as ‘non-saline’, with negligible crop effects. These results indicate that the restoration designed to enhance fish habitat resulted in limited salinity intrusion to the adjacent cropland. This study, along with concurrent projects in the Swinomish agricultural area, suggests that fish and farming, two economically and culturally significant symbols of the region, may not only survive, but thrive in the same space

Minimizing the stabbing number of matchings, trees, and triangulations

The (axis-parallel) stabbing number of a given set of line segments is the maximum number of segments that can be intersected by any one (axis-parallel) line. This paper deals with finding perfect matchings, spanning trees, or triangulations of minimum stabbing number for a given set of points. The complexity of these problems has been a long-standing open question; in fact, it is one of the original 30 outstanding open problems in computational geometry on the list by Demaine, Mitchell, and O'Rourke. The answer we provide is negative for a number of minimum stabbing problems by showing them NP-hard by means of a general proof technique. It implies non-trivial lower bounds on the approximability. On the positive side we propose a cut-based integer programming formulation for minimizing the stabbing number of matchings and spanning trees. We obtain lower bounds (in polynomial time) from the corresponding linear programming relaxations, and show that an optimal fractional solution always contains an edge of at least constant weight. This result constitutes a crucial step towards a constant-factor approximation via an iterated rounding scheme. In computational experiments we demonstrate that our approach allows for actually solving problems with up to several hundred points optimally or near-optimally.Comment: 25 pages, 12 figures, Latex. To appear in "Discrete and Computational Geometry". Previous version (extended abstract) appears in SODA 2004, pp. 430-43

Collapsing granular suspensions

A 2D contact dynamics model is proposed as a microscopic description of a collapsing suspension/soil to capture the essential physical processes underlying the dynamics of generation and collapse of the system. Our physical model is compared with real data obtained from in situ measurements performed with a natural collapsing/suspension soil. We show that the shear strength behavior of our collapsing suspension/soil model is very similar to the behavior of this collapsing suspension soil, for both the unperturbed and the perturbed phases of the material.Comment: 7 pages, 5 figures, accepted for publication in EPJ

Connexin43 Inhibition Prevents Human Vein Grafts Intimal Hyperplasia.

Venous bypass grafts often fail following arterial implantation due to excessive smooth muscle cells (VSMC) proliferation and consequent intimal hyperplasia (IH). Intercellular communication mediated by Connexins (Cx) regulates differentiation, growth and proliferation in various cell types. Microarray analysis of vein grafts in a model of bilateral rabbit jugular vein graft revealed Cx43 as an early upregulated gene. Additional experiments conducted using an ex-vivo human saphenous veins perfusion system (EVPS) confirmed that Cx43 was rapidly increased in human veins subjected ex-vivo to arterial hemodynamics. Cx43 knock-down by RNA interference, or adenoviral-mediated overexpression, respectively inhibited or stimulated the proliferation of primary human VSMC in vitro. Furthermore, Cx blockade with carbenoxolone or the specific Cx43 inhibitory peptide 43gap26 prevented the burst in myointimal proliferation and IH formation in human saphenous veins. Our data demonstrated that Cx43 controls proliferation and the formation of IH after arterial engraftment