Tautomerism in large databases

We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS’s tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection

Suppressing Electroweak Precision Observables in 5D Warped Models

We elaborate on a recently proposed mechanism to suppress large contributions to the electroweak precision observables in five dimensional (5D) warped models, without the need for an extended 5D gauge sector. The main ingredient is a modification of the AdS metric in the vicinity of the infrared (IR) brane corresponding to a strong deviation from conformality in the IR of the 4D holographic dual. We compute the general low energy effective theory of the 5D warped Standard Model, emphasizing additional IR contributions to the wave function renormalization of the light Higgs mode. We also derive expressions for the S and T parameters as a function of a generic 5D metric and zero-mode wave functions. We give an approximate formula for the mass of the radion that works even for strong deviation from the AdS background. We proceed to work out the details of an explicit model and derive bounds for the first KK masses of the various bulk fields. The radion is the lightest new particle although its mass is already at about 1/3 of the mass of the lightest resonances, the KK states of the gauge bosons. We examine carefully various issues that can arise for extreme choices of parameters such as the possible reintroduction of the hierarchy problem, the onset of nonperturbative physics due to strong IR curvature or the creation of new hierarchies near the Planck scale. We conclude that a KK scale of 1 TeV is compatible with all these constraints.Comment: 44 pages, 11 figures, references adde

Ants, Cataglyphis cursor, Use Precisely Directed Rescue Behavior to Free Entrapped Relatives

Although helping behavior is ubiquitous throughout the animal kingdom, actual rescue activity is particularly rare. Nonetheless, here we report the first experimental evidence that ants, Cataglyphis cursor, use precisely directed rescue behavior to free entrapped victims; equally important, they carefully discriminate between individuals in distress, offering aid only to nestmates. Our experiments simulate a natural situation, which we often observed in the field when collecting Catagyphis ants, causing sand to collapse in the process. Using a novel experimental technique that binds victims experimentally, we observed the behavior of separate, randomly chosen groups of 5 C. cursor nestmates under one of six conditions. In five of these conditions, a test stimulus (the “victim”) was ensnared with nylon thread and held partially beneath the sand. The test stimulus was either (1) an individual from the same colony; (2) an individual from a different colony of C cursor; (3) an ant from a different ant species; (4) a common prey item; or, (5) a motionless (chilled) nestmate. In the final condition, the test stimulus (6) consisted of the empty snare apparatus. Our results demonstrate that ants are able to recognize what, exactly, holds their relative in place and direct their behavior to that object, the snare, in particular. They begin by excavating sand, which exposes the nylon snare, transporting sand away from it, and then biting at the snare itself. Snare biting, a behavior never before reported in the literature, demonstrates that rescue behavior is far more sophisticated, exact and complexly organized than the simple forms of helping behavior already known, namely limb pulling and sand digging. That is, limb pulling and sand digging could be released directly by a chemical call for help and thus result from a very simple mechanism. However, it's difficult to see how this same releasing mechanism could guide rescuers to the precise location of the nylon thread, and enable them to target their bites to the thread itself

SUSY Splits, But Then Returns

We study the phenomenon of accidental or "emergent" supersymmetry within gauge theory and connect it to the scenarios of Split Supersymmetry and Higgs compositeness. Combining these elements leads to a significant refinement and extension of the proposal of Partial Supersymmetry, in which supersymmetry is broken at very high energies but with a remnant surviving to the weak scale. The Hierarchy Problem is then solved by a non-trivial partnership between supersymmetry and compositeness, giving a promising approach for reconciling Higgs naturalness with the wealth of precision experimental data. We discuss aspects of this scenario from the AdS/CFT dual viewpoint of higher-dimensional warped compactification. It is argued that string theory constructions with high scale supersymmetry breaking which realize warped/composite solutions to the Hierarchy Problem may well be accompanied by some or all of the features described. The central phenomenological considerations and expectations are discussed, with more detailed modelling within warped effective field theory reserved for future work.Comment: 29 pages. Flavor and CP constraints on left-right symmetric structure briefly discussed. References adde

Supersymmetry with Light Stops

Recent LHC data, together with the electroweak naturalness argument, suggest that the top squarks may be significantly lighter than the other sfermions. We present supersymmetric models in which such a split spectrum is obtained through "geometries": being "close to" electroweak symmetry breaking implies being "away from" supersymmetry breaking, and vice versa. In particular, we present models in 5D warped spacetime, in which supersymmetry breaking and Higgs fields are located on the ultraviolet and infrared branes, respectively, and the top multiplets are localized to the infrared brane. The hierarchy of the Yukawa matrices can be obtained while keeping near flavor degeneracy between the first two generation sfermions, avoiding stringent constraints from flavor and CP violation. Through the AdS/CFT correspondence, the models can be interpreted as purely 4D theories in which the top and Higgs multiplets are composites of some strongly interacting sector exhibiting nontrivial dynamics at a low energy. Because of the compositeness of the Higgs and top multiplets, Landau pole constraints for the Higgs and top couplings apply only up to the dynamical scale, allowing for a relatively heavy Higgs boson, including m_h = 125 GeV as suggested by the recent LHC data. We analyze electroweak symmetry breaking for a well-motivated subset of these models, and find that fine-tuning in electroweak symmetry breaking is indeed ameliorated. We also discuss a flat space realization of the scenario in which supersymmetry is broken by boundary conditions, with the top multiplets localized to a brane while other matter multiplets delocalized in the bulk.Comment: 27 pages, 7 figure

Cisplatin-induced emesis: systematic review and meta-analysis of the ferret model and the effects of 5-HT3 receptor antagonists

PURPOSE: The ferret cisplatin emesis model has been used for ~30 years and enabled identification of clinically used anti-emetics. We provide an objective assessment of this model including efficacy of 5-HT(3) receptor antagonists to assess its translational validity. METHODS: A systematic review identified available evidence and was used to perform meta-analyses. RESULTS: Of 182 potentially relevant publications, 115 reported cisplatin-induced emesis in ferrets and 68 were included in the analysis. The majority (n = 53) used a 10 mg kg(−1) dose to induce acute emesis, which peaked after 2 h. More recent studies (n = 11) also used 5 mg kg(−1), which induced a biphasic response peaking at 12 h and 48 h. Overall, 5-HT(3) receptor antagonists reduced cisplatin (5 mg kg(−1)) emesis by 68% (45–91%) during the acute phase (day 1) and by 67% (48–86%) and 53% (38–68%, all P < 0.001), during the delayed phase (days 2, 3). In an analysis focused on the acute phase, the efficacy of ondansetron was dependent on the dosage and observation period but not on the dose of cisplatin. CONCLUSION: Our analysis enabled novel findings to be extracted from the literature including factors which may impact on the applicability of preclinical results to humans. It reveals that the efficacy of ondansetron is similar against low and high doses of cisplatin. Additionally, we showed that 5-HT(3) receptor antagonists have a similar efficacy during acute and delayed emesis, which provides a novel insight into the pharmacology of delayed emesis in the ferret

A Survey on Continuous Time Computations

We provide an overview of theories of continuous time computation. These theories allow us to understand both the hardness of questions related to continuous time dynamical systems and the computational power of continuous time analog models. We survey the existing models, summarizing results, and point to relevant references in the literature

CSF from Parkinson disease Patients Differentially Affects Cultured Microglia and Astrocytes

<p>Abstract</p> <p>Background</p> <p>Excessive and abnormal accumulation of alpha-synuclein (α-synuclein) is a factor contributing to pathogenic cell death in Parkinson's disease. The purpose of this study, based on earlier observations of Parkinson's disease cerebrospinal fluid (PD-CSF) initiated cell death, was to determine the effects of CSF from PD patients on the functionally different microglia and astrocyte glial cell lines. Microglia cells from human glioblastoma and astrocytes from fetal brain tissue were cultured, grown to confluence, treated with fixed concentrations of PD-CSF, non-PD disease control CSF, or control no-CSF medium, then photographed and fluorescently probed for α-synuclein content by deconvolution fluorescence microscopy. Outcome measures included manually counted cell growth patterns from day 1-8; α-synuclein density and distribution by antibody tagged 3D model stacked deconvoluted fluorescent imaging.</p> <p>Results</p> <p>After PD-CSF treatment, microglia growth was reduced extensively, and a non-confluent pattern with morphological changes developed, that was not evident in disease control CSF and no-CSF treated cultures. Astrocyte growth rates were similarly reduced by exposure to PD-CSF, but morphological changes were not consistently noted. PD-CSF treated microglia showed a significant increase in α-synuclein content by day 4 compared to other treatments (p ≤ 0.02). In microglia only, α-synuclein aggregated and redistributed to peri-nuclear locations.</p> <p>Conclusions</p> <p>Cultured microglia and astrocytes are differentially affected by PD-CSF exposure compared to non-PD-CSF controls. PD-CSF dramatically impacts microglia cell growth, morphology, and α-synuclein deposition compared to astrocytes, supporting the hypothesis of cell specific susceptibility to PD-CSF toxicity.</p

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns