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

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.]

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

Some topics in theoretical population genetics: Editorial commentaries on a selection of Marc Feldman's TPB papers.

This article consists of commentaries on a selected group of papers of Marc Feldman published in Theoretical Population Biology from 1970 to the present. The papers describe a diverse set of population-genetic models, covering topics such as cultural evolution, social evolution, and the evolution of recombination. The commentaries highlight Marc Feldman's role in providing mathematically rigorous formulations to explore qualitative hypotheses, in many cases generating surprising conclusions

Sexual Dysfunction in Jordanian Diabetic Women

OBJECTIVE—To estimate the prevalence of female sexual dysfunction (FSD) in diabetic and nondiabetic Jordanian women

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr- TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr- TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/

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

"Actual" does not imply "feasible"

The familiar complaint that some ambitious proposal is infeasible naturally invites the following response: Once upon a time, the abolition of slavery and the enfranchisement of women seemed infeasible, yet these things were actually achieved. Presumably, then, many of those things that seem infeasible in our own time may well be achieved too and, thus, turn out to have been perfectly feasible after all. The Appeal to History, as we call it, is a bad argument. It is not true that if some desirable state of affairs was actually achieved, then it was feasible that it was achieved. “Actual” does not imply “feasible,” as we put it. Here is our objection. “Feasible” implies “not counterfactually fluky.” But “actual” does not imply “not counterfactually fluky.” So, “actual” does not imply “feasible.” While something like the Flukiness Objection is sometimes hinted at in the context of the related literature on abilities, it has not been developed in any detail, and both premises are inadequately motivated. We offer a novel articulation of the Flukiness Objection that is both more precise and better motivated. Our conclusions have important implications, not only for the admissible use of history in normative argument, but also by potentially circumscribing the normative claims that are applicable to us

Hard-boiled Ecologies: Ross Macdonald’s Environmental Crime Fiction

Although Ross Macdonald’s position in the annals of great American hardboiled crime writers is unquestioned, what often been overlooked in the study of his works are the underlying environmental preoccupations that frequently serve as the background to, or context for, crime. This context of ecological violence is forcefully manifested in two of Macdonald’s later Archer novels The Underground Man (1971) and Sleeping Beauty (1973). This essay scrutinizes the environmental imperatives of Macdonald’s work, arguing that the damage and destruction inflicted upon the environment in these two texts becomes symbiotically connected to the broader, morally fraught social milieu of the city