Rationality as the Rule of Reason

The demands of rationality are linked both to our subjective normative perspective (given that rationality is a person-level concept) and to objective reasons or favoring relations (given that rationality is non-contingently authoritative for us). In this paper, I propose a new way of reconciling the tension between these two aspects: roughly, what rationality requires of us is having the attitudes that correspond to our take on reasons in the light of our evidence, but only if it is competent. I show how this view can account for structural rationality on the assumption that intentions and beliefs as such involve competent perceptions of downstream reasons, and explore various implications of the account

Selection of Post-Acute Care for Stroke Patients

Background: Significant variation exists in post-acute care for stroke survivors. This study examines referral practices of occupational and physical therapists for patients after acute stroke. Method: Occupational therapists (OTs) and physical therapists (PTs) were surveyed either electronically or in person at a national conference. The respondents selected the most appropriate referral for each of five case vignettes. The referral choices included Inpatient Rehabilitation Facility (IRF), Skilled Nursing Facility (SNF), Long-Term Acute Care Hospital (LTACH), home with home services, or home with outpatient services. Demographic data included practice location, setting, and duration. The respondents were also asked to rate how strongly 15 clinical factors influence their referral decisions. Results: The 33 OTs and 41 PTs favored similar referrals. Consensus was observed in four of the five cases. No differences were observed among the respondents based on practice location, practice setting, or number of years in practice and the referrals. Prognosis for functional improvement and pre-stroke functional status were identified as the most important factors influencing referral decisions. Conclusion: Further studies are needed to define areas of broad consensus as well as areas of disagreement, with subsequent efforts to clarify optimal treatment algorithms for patients who currently receive variable rehabilitative care

R3D-BLAST: a search tool for similar RNA 3D substructures

R3D-BLAST is a BLAST-like search tool that allows the user to quickly and accurately search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. The basic idea behind R3D-BLAST is that all the RNA 3D structures deposited in the PDB are first encoded as 1D structural sequences using a structural alphabet of 23 distinct nucleotide conformations, and BLAST is then applied to these 1D structural sequences to search for those RNA substructures whose 1D structural sequences are similar to that of the query RNA substructure. R3D-BLAST takes as input an RNA 3D structure in the PDB format and outputs all substructures of the hits similar to that of the query with a graphical display to show their structural superposition. In addition, each RNA substructure hit found by R3D-BLAST has an associated E-value to measure its statistical significance. R3D-BLAST is now available online at http://genome.cs.nthu.edu.tw/R3D-BLAST/ for public access

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time

The pacing stress test: Thallium-201 myocardial imaging after atrial pacing. Diagnostic value in detecting coronary artery disease compared with exercise testing

Many patients suspected of having coronary artery disease are unable to undergo adequate exercise testing. An alternate stress, pacing tachycardia, has been shown to produce electrocardiographic changes that are as sensitive and specific as those observed during exercise testing. To compare thallium-201 imaging after atrial pacing stress with thallium imaging after exercise stress, 22 patients undergoing cardiac catheterization were studied with both standard exercise thallium imaging and pacing thallium imaging.Positive ischemic electrocardiographic changes (> 1 mm ST segment depression) were noted in 11 of 16 patients with coronary artery disease during exercise, and in 15 of the 16 patients during atrial pacing. One of six patients with normal or trivial coronary artery disease had a positive electrocardiogram with each test. Exercise thallium imaging was positive in 13 of 16 patients with coronary artery disease compared with 15 of 16 patients during atrial pacing. Three of six patients without coronary artery disease had a positive scan with exercise testing, and two of these same patients developed a positive scan with atrial pacing. Of those patients with coronary artery disease and an abnormal scan, 85% showed redistribution with exercise testing compared with 87% during atrial pacing. Segment by segment comparison of thallium imaging after either atrial pacing or exercise showed that there was a good correlation of the location and severity of the thallium defects (r = 0.83, p = 0.0001, Spearman rank correlation).It is concluded that the location and presence of both fixed and transient thallium defects after atrial pacing are closely correlated with the findings after exercise testing. Thus, atrial pacing may be used as a stress for myocardial perfusion scintigraphy in patients unable to complete a satisfactory exercise test

MarkUs: a server to navigate sequence–structure–function space

We describe MarkUs, a web server for analysis and comparison of the structural and functional properties of proteins. In contrast to a ‘structure in/function out’ approach to protein function annotation, the server is designed to be highly interactive and to allow flexibility in the examination of possible functions, suggested either automatically by various similarity measures or specified by a user directly. This is combined with tools that allow a user to assess independently whether or not a suggested function is consistent with the bioinformatic and biophysical properties of a given query structure, further allowing the user to generate testable hypotheses. The server is available at http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us

Coupling effects in QD dimers at sub-nanometer interparticle distance

Currently, intensive research efforts focus on the fabrication of meso-structures of assembled colloidal quantum dots (QDs) with original optical and electronic properties. Such collective features originate from the QDs coupling, depending on the number of connected units and their distance. However, the development of general methodologies to assemble colloidal QD with precise stoichiometry and particle-particle spacing remains a key challenge. Here, we demonstrate that dimers of CdSe QDs, stable in solution, can be obtained by engineering QD surface chemistry, reducing the surface steric hindrance and favoring the link between two QDs. The connection is made by using alkyl dithiols as bifunctional linkers and different chain lengths are used to tune the interparticle distance from few nm down to 0.5 nm. The spectroscopic investigation highlights that coupling phenomena between the QDs in dimers are strongly dependent on the interparticle distance and QD size, ultimately affecting the exciton dissociation efficiency. [Figure not available: see fulltext.]

Nuclear medicine procedures and the evaluation of male sexual organs: a short review

Sexuality consists of three aspects that are interrelated and inseparable, biological, physiological and social. The biological aspect considers the individual's capability to give and to receive pleasure. In consequence, it covers the functionality of the sexual organs and the physiology of human sexual response cycle. Diagnostic imaging modalities, such as single photon emission computed tomography (SPECT) and positron emission tomography (PET) have been used to evaluate clinical disorders of the male reproductive system. PET and SPECT procedures basically involve the administration of a radiopharmaceutical that has a higher uptake in a specific tumor or tissue. The aim of this brief review is to present some radiopharmaceuticals that have been used in the clinical evaluation of the male sexual organs (testes, prostate, seminal vesicles, penis) related with male sexuality. This information could be useful in better understanding the male sexual response cycle, as well as the sexual disorders, when considering the male sexual organs and the pelvic floor. Moreover, the findings obtained with PET and SPECT imaging could help to evaluate the efficacy of clinical results of therapeutic procedures. In conclusion, the knowledge from these images could aid in better understanding the physiology of the different organs related with sexuality. Furthermore, they could be important tools to evaluate the physiological integrity of the involved organs, to improve clinical strategies and to accompany the patients under treatment

Convergent algorithms for protein structural alignment

<p>Abstract</p> <p>Background</p> <p>Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural similarities. However, current practical methods are seldom supported by convergence theories. In particular, although the goal of each algorithm is to maximize some scoring function, there is no practical method that theoretically guarantees score maximization. A practical algorithm with solid convergence properties would be useful for the refinement of protein folding maps, and for the development of new scores designed to be correlated with functional similarity.</p> <p>Results</p> <p>In this work, the maximization of scoring functions in protein alignment is interpreted as a Low Order Value Optimization (LOVO) problem. The new interpretation provides a framework for the development of algorithms based on well established methods of continuous optimization. The resulting algorithms are convergent and <it>increase the scoring functions at every iteration</it>. The solutions obtained are critical points of the scoring functions. Two algorithms are introduced: One is based on the maximization of the scoring function with Dynamic Programming followed by the continuous maximization of <it>the same </it>score, with respect to the protein position, using a smooth Newtonian method. The second algorithm replaces the Dynamic Programming step by a fast procedure for computing the correspondence between C<it>α </it>atoms. The algorithms are shown to be very effective for the maximization of the STRUCTAL score.</p> <p>Conclusion</p> <p>The interpretation of protein alignment as a LOVO problem provides a new theoretical framework for the development of convergent protein alignment algorithms. These algorithms are shown to be very reliable for the maximization of the STRUCTAL score, and other distance-dependent scores may be optimized with same strategy. The improved score optimization provided by these algorithms provide means for the refinement of protein fold maps and also for the development of scores designed to match biological function. The LOVO strategy may be also used for more general structural superposition problems such as flexible or non-sequential alignments. The package is available on-line at http://www.ime.unicamp.br/~martinez/lovoalign.</p