Reflection of X-rays with change of frequency. Part IV. Rock salt

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Quantum theory of X-ray reflection: experimental confirmation

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IDSS: deformation invariant signatures for molecular shape comparison

<p>Abstract</p> <p>Background</p> <p>Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC) treat them as rigid bodies, which may lead to incorrect measure of the shape similarity of flexible molecules.</p> <p>Results</p> <p>To address the issue we introduce a new shape descriptor, called Inner Distance Shape Signature (IDSS), for describing the 3D shapes of flexible molecules. The inner distance is defined as the length of the shortest path between landmark points within the molecular shape, and it reflects well the molecular structure and deformation without explicit decomposition. Our IDSS is stored as a histogram which is a probability distribution of inner distances between all sample point pairs on the molecular surface. We show that IDSS is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. Our approach reduces the 3D shape comparison problem of flexible molecules to the comparison of IDSS histograms.</p> <p>Conclusion</p> <p>The proposed algorithm is robust and does not require any prior knowledge of the flexible regions. We demonstrate the effectiveness of IDSS within a molecular search engine application for a benchmark containing abundant conformational changes of molecules. Such comparisons in several thousands per second can be carried out. The presented IDSS method can be considered as an alternative and complementary tool for the existing methods for rigid MSC. The binary executable program for Windows platform and database are available from <url>https://engineering.purdue.edu/PRECISE/IDSS</url>.</p

DNA-Free Recombinant SV40 Capsids Protect Mice from Acute Renal Failure by Inducing Stress Response, Survival Pathway and Apoptotic Arrest

Viruses induce signaling and host defense during infection. Employing these natural trigger mechanisms to combat organ or tissue failure is hampered by harmful effects of most viruses. Here we demonstrate that SV40 empty capsids (Virus Like Particles-VLPs), with no DNA, induce host Hsp/c70 and Akt-1 survival pathways, key players in cellular survival mechanisms. We postulated that this signaling might protect against organ damage in vivo. Acute kidney injury (AKI) was chosen as target. AKI is critical, prevalent disorder in humans, caused by nephrotoxic agents, sepsis or ischemia, via apoptosis/necrosis of renal tubular cells, with high morbidity and mortality. Systemic administration of VLPs activated Akt-1 and upregulated Hsp/c70 in vivo. Experiments in mercury-induced AKI mouse model demonstrated that apoptosis, oxidative stress and toxic renal failure were significantly attenuated by pretreatment with capsids prior to the mercury insult. Survival rate increased from 12% to >60%, with wide dose response. This study demonstrates that SV40 VLPs, devoid of DNA, may potentially be used as prophylactic agent for AKI. We anticipate that these finding may be projected to a wide range of organ failure, using empty capsids of SV40 as well as other viruses

Shaping a screening file for maximal lead discovery efficiency and effectiveness: elimination of molecular redundancy

High Throughput Screening (HTS) is a successful strategy for finding hits and leads that have the opportunity to be converted into drugs. In this paper we highlight novel computational methods used to select compounds to build a new screening file at Pfizer and the analytical methods we used to assess their quality. We also introduce the novel concept of molecular redundancy to help decide on the density of compounds required in any region of chemical space in order to be confident of running successful HTS campaigns

Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: interaction cliffs.

This is the original submitted version, before peer review. The final peer-reviewed version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/ci500721x.Activity landscape modeling is mostly a descriptive technique that allows rationalizing continuous and discontinuous SARs. Nevertheless, the interpretation of some landscape features, especially of activity cliffs, is not straightforward. As the nature of activity cliffs depends on the ligand and the target, information regarding both should be included in the analysis. A specific way to include this information is using protein-ligand interaction fingerprints (IFPs). In this paper we report the activity landscape modeling of 507 ligand-kinase complexes (from the KLIFS database) including IFP, which facilitates the analysis and interpretation of activity cliffs. Here we introduce the structure-activity-interaction similarity (SAIS) maps that incorporate information on ligand-target contact similarity. We also introduce the concept of interaction cliffs defined as ligand-target complexes with high structural and interaction similarity but have a large potency difference of the ligands. Moreover, the information retrieved regarding the specific interaction allowed the identification of activity cliff hot spots, which help to rationalize activity cliffs from the target point of view. In general, the information provided by IFPs provides a structure-based understanding of some activity landscape features. This paper shows examples of analyses that can be carried out when IFPs are added to the activity landscape model.M-L is very grateful to CONACyT (No. 217442/312933) and the Cambridge Overseas Trust for funding. AB thanks Unilever for funding and the European Research Council for a Starting Grant (ERC-2013- StG-336159 MIXTURE). J.L.M-F. is grateful to the School of Chemistry, Department of Pharmacy of the National Autonomous University of Mexico (UNAM) for support. This work was supported by a scholarship from the Secretariat of Public Education and the Mexican government

Perspective taking and systematic biases in object location memory.

The aim of the current study was to develop a novel task that allows for the quick assessment of spatial memory precision with minimal technical and training requirements. In this task, participants memorized the position of an object in a virtual room and then judged from a different perspective, whether the object has moved to the left or to the right. Results revealed that participants exhibited a systematic bias in their responses that we termed the reversed congruency effect. Specifically, they performed worse when the camera and the object moved in the same direction than when they moved in opposite directions. Notably, participants responded correctly in almost 100% of the incongruent trials, regardless of the distance by which the object was displaced. In Experiment 2, we showed that this effect cannot be explained by the movement of the object on the screen, but that it relates to the perspective shift and the movement of the object in the virtual world. We also showed that the presence of additional objects in the environment reduces the reversed congruency effect such that it no longer predicts performance. In Experiment 3, we showed that the reversed congruency effect is greater in older adults, suggesting that the quality of spatial memory and perspective-taking abilities are critical. Overall, our results suggest that this effect is driven by difficulties in the precise encoding of object locations in the environment and in understanding how perspective shifts affect the projected positions of the objects in the two-dimensional image

Quantum X-ray reflection in diamond

It has been shown that, corresponding to the usual formula, equation for the classical or unmodified reflection of X-rays, the general geometric law of modified or quantum reflection by crystals is &#952; and &#968; are here the glancing angles of incidence on the static and dynamic stratifications measured in the respective planes of incidence, &amp;epsiv is the angle between these stratifications, and I the inclination of the phase-waves of the lattice vibration to the static crystal planes. The two planes of incidence would coincide when the equations are simultaneously satisfied, and more generally also when the observations are made in a plane of the symmetry of the crystal. We may then write 2 &#968; = (&#966; + &#952;) and 2 &amp;epsiv = (&#966; + &#952; ), where &#952; and &#966; are the glancing angles of incidence and of quantum reflection measured with reference to the static crystal planes. The angle I in equation (2) is thus capable of being evaluated directly from observations of the Laue and the quantum reflections over a sufficient range of incidences. If I is &#966;/2, equation (2) reduces to as a close approximation

Modified reflection of X-rays

As stated in an earlier communication, quantum theory leads to the remarkable conclusion that the reflection of X-rays in crystals is of two types; first, the classical or unmodified reflections associated with the normal structure amplitudes of the crystal; and secondly, the quantum or modified reflections which arise when the vibrations of the crystal lattice are quantum-mechanically excited by the incident X-radiation. The direction and intensity of the reflections of the second kind have been considered theoretically in a recent paper. It is shown that when the energy taken up by the crystal lattice is in the form of acoustic waves, the recoil of the photon is observable as a diffuse scattering of the incident X-radiation, while on the other hand, when the optical vibrations of the crystal lattice are excited, the resulting effect is a regular reflection of the incident radiation