On sutured Floer homology and the equivalence of Seifert surfaces

We study the sutured Floer homology invariants of the sutured manifold obtained by cutting a knot complement along a Seifert surface, R. We show that these invariants are finer than the "top term" of the knot Floer homology, which they contain. In particular, we use sutured Floer homology to distinguish two non-isotopic minimal genus Seifert surfaces for the knot 8_3. A key ingredient for this technique is finding appropriate Heegaard diagrams for the sutured manifold associated to the complement of a Seifert surface.Comment: 32 pages, 17 figure

Time-Resolved Ultrafast Transient Polarization Spectroscopy to Investigate Nonlinear Processes and Dynamics in Electronically Excited Molecules on the Femtosecond Time Scale

We report a novel experimental technique to investigate ultrafast dynamics in photoexcited molecules by probing the third-order nonlinear optical susceptibility. A non-colinear 3-pulse scheme is developed to probe the ultrafast dynamics of excited electronic states using the optical Kerr effect by time-resolved polarization spectroscopy. Optical heterodyne and optical homodyne detection are demonstrated to measure the third-order nonlinear optical response for the S1 excited state of liquid nitrobenzene, which is populated by 2-photon absorption of a 780 nm 35 fs excitation pulse.Comment: 12 pages, 4 figures. Changes from previous version: added panel labels to figures 3-

Ultrafast Dynamics of Excited Electronic States in Nitrobenzene Measured by Ultrafast Transient Polarization Spectroscopy.

We investigate ultrafast dynamics of the lowest singlet excited electronic state in liquid nitrobenzene using ultrafast transient polarization spectroscopy, extending the well-known technique of optical Kerr effect spectroscopy to excited electronic states. The third-order nonlinear response of the excited molecular ensemble is measured using a pair of femtosecond pulses following a third femtosecond pulse that populates the S1 excited state. By measuring this response, which is highly sensitive to details of the excited state character and structure, as a function of time delays between the three pulses involved, we extract the dephasing time of the wave packet on the excited state. The dephasing time, measured as a function of time delay after pump excitation, shows oscillations indicating oscillatory wave packet dynamics on the excited state. From the experimental measurements and supporting theoretical calculations, we deduce that the wave packet completely leaves the S1 state potential energy surface after three traversals of the intersystem crossing between the singlet S1 and triplet T2 states

Topological Chaos in Spatially Periodic Mixers

Topologically chaotic fluid advection is examined in two-dimensional flows with either or both directions spatially periodic. Topological chaos is created by driving flow with moving stirrers whose trajectories are chosen to form various braids. For spatially periodic flows, in addition to the usual stirrer-exchange braiding motions, there are additional topologically-nontrivial motions corresponding to stirrers traversing the periodic directions. This leads to a study of the braid group on the cylinder and the torus. Methods for finding topological entropy lower bounds for such flows are examined. These bounds are then compared to numerical stirring simulations of Stokes flow to evaluate their sharpness. The sine flow is also examined from a topological perspective.Comment: 18 pages, 14 figures. RevTeX4 style with psfrag macros. Final versio

Statistical competencies for medical research learners: What is fundamental?

IntroductionIt is increasingly essential for medical researchers to be literate in statistics, but the requisite degree of literacy is not the same for every statistical competency in translational research. Statistical competency can range from 'fundamental' (necessary for all) to 'specialized' (necessary for only some). In this study, we determine the degree to which each competency is fundamental or specialized.MethodsWe surveyed members of 4 professional organizations, targeting doctorally trained biostatisticians and epidemiologists who taught statistics to medical research learners in the past 5 years. Respondents rated 24 educational competencies on a 5-point Likert scale anchored by 'fundamental' and 'specialized.'ResultsThere were 112 responses. Nineteen of 24 competencies were fundamental. The competencies considered most fundamental were assessing sources of bias and variation (95%), recognizing one's own limits with regard to statistics (93%), identifying the strengths, and limitations of study designs (93%). The least endorsed items were meta-analysis (34%) and stopping rules (18%).ConclusionWe have identified the statistical competencies needed by all medical researchers. These competencies should be considered when designing statistical curricula for medical researchers and should inform which topics are taught in graduate programs and evidence-based medicine courses where learners need to read and understand the medical research literature

Topology of Chaotic Mixing Patterns

A stirring device consisting of a periodic motion of rods induces a mapping of the fluid domain to itself, which can be regarded as a homeomorphism of a punctured surface. Having the rods undergo a topologically-complex motion guarantees at least a minimum amount of stretching of material lines, which is important for chaotic mixing. We use topological considerations to describe the nature of the injection of unmixed material into a central mixing region, which takes place at injection cusps. A topological index formula allow us to predict the possible types of unstable foliations that can arise for a fixed number of rods.Comment: 15 pages, 13 figures, RevTeX4 macros. Final versio

Activity of the DNA minor groove cross-linking agent SG2000 (SJG-136) against canine tumours

BACKGROUND: Cancer is the leading cause of death in older dogs and its prevalence is increasing. There is clearly a need to develop more effective anti-cancer drugs in dogs. SG2000 (SJG-136) is a sequence selective DNA minor groove cross-linking agent. Based on its in vitro potency, the spectrum of in vivo and clinical activity against human tumours, and its tolerability in human patients, SG2000 has potential as a novel therapeutic against spontaneously occurring canine malignancies. RESULTS: In vitro cytotoxicity was assessed using SRB and MTT assays, and in vivo activity was assessed using canine tumour xenografts. DNA interstrand cross-linking (ICL) was determined using a modification of the single cell gel electrophoresis (comet) assay. Effects on cell cycle distribution were assessed by flow cytometry and measurement of γ-H2AX by immunofluorescence and immunohistochemistry. SG2000 had a multi-log differential cytotoxic profile against a panel of 12 canine tumour cell lines representing a range of common tumour types in dogs. In the CMeC-1 melanoma cell line, DNA ICLs increased linearly with dose following a 1 h treatment. Peak ICL was achieved within 1 h and no removal was observed over 48 h. A relationship between DNA ICL formation and cytotoxicity was observed across cell lines. The formation of γ-H2AX foci was slow, becoming evident after 4 h and reaching a peak at 24 h. SG2000 exhibited significant anti-tumour activity against two canine melanoma tumour models in vivo. Anti-tumour activity was observed at 0.15 and 0.3 mg/kg given i.v. either once, or weekly x 3. Dose-dependent DNA ICL was observed in tumours (and to a lower level in peripheral blood mononuclear cells) at 2 h and persisted at 24 h. ICL increased following the second and third doses in a repeated dose schedule. At 24 h, dose dependent γ-H2AX foci were more numerous than at 2 h, and greater in tumours than in peripheral blood mononuclear cells. SG2000-induced H2AX phosphorylation measured by immunohistochemistry showed good correspondence, but less sensitivity, than measurement of foci. CONCLUSIONS: SG2000 displayed potent activity in vitro against canine cancer cell lines as a result of the formation and persistence of DNA ICLs. SG2000 also had significant in vivo antitumour activity against canine melanoma xenografts, and the comet and γ-H2AX foci methods were relevant pharmacodynamic assays. The clinical testing of SG2000 against spontaneous canine cancer is warranted. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0534-2) contains supplementary material, which is available to authorized users

The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay.

BACKGROUND: The fish pathogen Aliivibrio salmonicida is the causative agent of cold-water vibriosis in marine aquaculture. The Gram-negative bacterium causes tissue degradation, hemolysis and sepsis in vivo. RESULTS: In total, 4 286 protein coding sequences were identified, and the 4.6 Mb genome of A. salmonicida has a six partite architecture with two chromosomes and four plasmids. Sequence analysis revealed a highly fragmented genome structure caused by the insertion of an extensive number of insertion sequence (IS) elements. The IS elements can be related to important evolutionary events such as gene acquisition, gene loss and chromosomal rearrangements. New A. salmonicida functional capabilities that may have been aquired through horizontal DNA transfer include genes involved in iron-acquisition, and protein secretion and play potential roles in pathogenicity. On the other hand, the degeneration of 370 genes and consequent loss of specific functions suggest that A. salmonicida has a reduced metabolic and physiological capacity in comparison to related Vibrionaceae species. CONCLUSION: Most prominent is the loss of several genes involved in the utilisation of the polysaccharide chitin. In particular, the disruption of three extracellular chitinases responsible for enzymatic breakdown of chitin makes A. salmonicida unable to grow on the polymer form of chitin. These, and other losses could restrict the variety of carrier organisms A. salmonicida can attach to, and associate with. Gene acquisition and gene loss may be related to the emergence of A. salmonicida as a fish pathogen

Habits of Mind: Designing Courses for Student Success

Although content knowledge remains at the heart of college teaching and learning, forward-thinking instructors recognize that we must also provide 21st-century college students with transferable skills (sometimes called portable intellectual abilities) to prepare them for their futures (Vazquez, 2020; Ritchhart, 2015; Venezia & Jaeger, 2013; Hazard, 2012). To “grow their capacity as efficacious thinkers to navigate and thrive in the face of unprecedented change” (Costa et al., 2023), students must learn and improve important study skills and academic dispositions throughout their educational careers. If we do not focus on skills-building in college courses, students will not be prepared for the challenges that await them after they leave institutions of higher education. If students are not prepared for these postsecondary education challenges, then it is fair to say that college faculty have failed them