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In examining the influence that Henri Drouot had on historians of early modern France in the English speaking world, this article shows that his work formed an essential reference for anyone seeking to make sense of the French Wars of Religion. Although no-one within this group adopted his well-known thesis of the "bourgeoisie seconde" in order to understand the League movement as it played out in different provincial cities, all of them nevertheless have turned to Mayenne et la Bourgogne as an important model for understanding the relationship between social interests and political action that it has been necessary to address. The number of citations of Drouot's works has therefore increased steadily with the development of the profession as a whole, and numerous North American scholars of France have pointed to the importance of his example for their own work.

New higher-count-rate, integrating, large area X-ray detectors with framing rates as high as 17,400 images per second are beginning to be available. These will soon be used for specialized MX experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information? To explore this question, we have considered several approaches: summing short sequences of images, binning to create the effect of larger pixels, use of JPEG-2000 lossy wavelet-based compression, and use of Hcompress, which is a Haar-wavelet-based lossy compression borrowed from astronomy. We also explore the effect of the combination of summing, binning, and Hcompress or JPEG-2000. In each of these last two methods one can specify approximately how much one wants the result to be compressed from the starting file size. These provide particularly effective lossy compressions that retain essential information for structure solution from Bragg reflections., Synopsis: New higher-count-rate, integrating, large area X-ray detectors with framing rates as high as 17,400 images per second are beginning to be available. These will soon be used for specialized MX experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information?

Structural biology experiments benefit significantly from state-of-the-art synchrotron data collection. One can acquire macromolecular crystallography (MX) diffraction data on large-area photon-counting pixel-array detectors at framing rates exceeding 1000 frames per second, using 200 Gbps network connectivity, or higher when available. In extreme cases this represents a raw data throughput of about 25 GB s -1 , which is nearly impossible to deliver at reasonable cost without compression. Our field has used lossless compression for decades to make such data collection manageable. Many MX beamlines are now fitted with DECTRIS Eiger detectors, all of which are delivered with optimized compression algorithms by default, and they perform well with current framing rates and typical diffraction data. However, better lossless compression algorithms have been developed and are now available to the research community. Here one of the latest and most promising lossless compression algorithms is investigated on a variety of diffraction data like those routinely acquired at state-of-the-art MX beamlines., (open access.)

Macromolecular crystallography contributes significantly to understanding diseases and, more importantly, how to treat them by providing atomic resolution 3D structures of proteins. This is achieved by collecting X-ray diffraction images of protein crystals from important biological pathways. Spotfinders are used to detect the presence of crystals with usable data, and the spots from such crystals are the primary data used to solve the relevant structures. Having fast and accurate spot finding is essential, but recent advances in synchrotron beamlines used to generate X-ray diffraction images have brought us to the limits of what the best existing spotfinders can do. This bottleneck must be removed so spotfinder software can keep pace with the X-ray beamline hardware improvements and be able to see the weak or diffuse spots required to solve the most challenging problems encountered when working with diffraction images. In this paper, we first present Bragg Spot Detection (BSD), a large benchmark Bragg spot image dataset that contains 304 images with more than 66 000 spots. We then discuss the open source extensible U-Net-based spotfinder Bragg Spot Finder (BSF), with image pre-processing, a U-Net segmentation backbone, and post-processing that includes artifact removal and watershed segmentation. Finally, we perform experiments on the BSD benchmark and obtain results that are (in terms of accuracy) comparable to or better than those obtained with two popular spotfinder software packages ( Dozor and DIALS ), demonstrating that this is an appropriate framework to support future extensions and improvements., (© Jianxiang Dong et al. 2024.)

A method is proposed for choosing unit cells for a group of crystals so that they all appear as nearly similar as possible to a selected cell. Related unit cells with varying cell parameters or indexed with different lattice centering can be accommodated., (open access.)

Characterization of crystallographic lattices is an important tool in structure solution, crystallographic database searches and clustering of diffraction images in serial crystallography. Characterization of lattices by Niggli-reduced cells (based on the three shortest non-coplanar lattice vectors) or by Delaunay-reduced cells (based on four non-coplanar vectors summing to zero and all meeting at obtuse or right angles) is commonly performed. The Niggli cell derives from Minkowski reduction. The Delaunay cell derives from Selling reduction. All are related to the Wigner-Seitz (or Dirichlet, or Voronoi) cell of the lattice, which consists of the points at least as close to a chosen lattice point as they are to any other lattice point. The three non-coplanar lattice vectors chosen are here called the Niggli-reduced cell edges. Starting from a Niggli-reduced cell, the Dirichlet cell is characterized by the planes determined by 13 lattice half-edges: the midpoints of the three Niggli cell edges, the six Niggli cell face-diagonals and the four body-diagonals, but seven of the lengths are sufficient: three edge lengths, the three shorter of each pair of face-diagonal lengths, and the shortest body-diagonal length. These seven are sufficient to recover the Niggli-reduced cell.

The highly automated macromolecular crystallography beamline AMX/17-ID-1 is an undulator-based high-intensity (>5 × 10 12  photons s -1 ), micro-focus (7 µm × 5 µm), low-divergence (1 mrad × 0.35 mrad) energy-tunable (5-18 keV) beamline at the NSLS-II, Brookhaven National Laboratory, Upton, NY, USA. It is one of the three life science beamlines constructed by the NIH under the ABBIX project and it shares sector 17-ID with the FMX beamline, the frontier micro-focus macromolecular crystallography beamline. AMX saw first light in March 2016 and started general user operation in February 2017. At AMX, emphasis has been placed on high throughput, high capacity, and automation to enable data collection from the most challenging projects using an intense micro-focus beam. Here, the current state and capabilities of the beamline are reported, and the different macromolecular crystallography experiments that are routinely performed at AMX/17-ID-1 as well as some plans for the near future are presented., (open access.)

KAMO and BLEND provide particularly effective tools to automatically manage the merging of large numbers of data sets from serial crystallography. The requirement for manual intervention in the process can be reduced by extending BLEND to support additional clustering options such as the use of more accurate cell distance metrics and the use of reflection-intensity correlation coefficients to infer `distances' among sets of reflections. This increases the sensitivity to differences in unit-cell parameters and allows clustering to assemble nearly complete data sets on the basis of intensity or amplitude differences. If the data sets are already sufficiently complete to permit it, one applies KAMO once and clusters the data using intensities only. When starting from incomplete data sets, one applies KAMO twice, first using unit-cell parameters. In this step, either the simple cell vector distance of the original BLEND or the more sensitive NCDist is used. This step tends to find clusters of sufficient size such that, when merged, each cluster is sufficiently complete to allow reflection intensities or amplitudes to be compared. One then uses KAMO again using the correlation between reflections with a common hkl to merge clusters in a way that is sensitive to structural differences that may not have perturbed the unit-cell parameters sufficiently to make meaningful clusters. Many groups have developed effective clustering algorithms that use a measurable physical parameter from each diffraction still or wedge to cluster the data into categories which then can be merged, one hopes, to yield the electron density from a single protein form. Since these physical parameters are often largely independent of one another, it should be possible to greatly improve the efficacy of data-clustering software by using a multi-stage partitioning strategy. Here, one possible approach to multi-stage data clustering is demonstrated. The strategy is to use unit-cell clustering until the merged data are sufficiently complete and then to use intensity-based clustering. Using this strategy, it is demonstrated that it is possible to accurately cluster data sets from crystals that have subtle differences., (open access.)

Methods of generating random unit-cell data for testing software are discussed. Working within the space S 6 appears to be the most expeditious., (© Andrews and Bernstein 2022.)

One often observes small but measurable differences in the diffraction data measured from different crystals of a single protein. These differences might reflect structural differences in the protein and may reveal the natural dynamism of the molecule in solution. Partitioning these mixed-state data into single-state clusters is a critical step that could extract information about the dynamic behavior of proteins from hundreds or thousands of single-crystal data sets. Mixed-state data can be obtained deliberately (through intentional perturbation) or inadvertently (while attempting to measure highly redundant single-crystal data). To the extent that different states adopt different molecular structures, one expects to observe differences in the crystals; each of the polystates will create a polymorph of the crystals. After mixed-state diffraction data have been measured, deliberately or inadvertently, the challenge is to sort the data into clusters that may represent relevant biological polystates. Here, this problem is addressed using a simple multi-factor clustering approach that classifies each data set using independent observables, thereby assigning each data set to the correct location in conformational space. This procedure is illustrated using two independent observables, unit-cell parameters and intensities, to cluster mixed-state data from chymotrypsinogen (ChTg) crystals. It is observed that the data populate an arc of the reaction trajectory as ChTg is converted into chymotrypsin., (open access.)

Here we present two robotic sample changers integrated into the experimental stations for the macromolecular crystallography (MX) beamlines AMX and FMX, and the biological small-angle scattering (bioSAXS) beamline LiX. They enable fully automated unattended data collection and remote access to the beamlines. The system designs incorporate high-throughput, versatility, high-capacity, resource sharing and robustness. All systems are centered around a six-axis industrial robotic arm coupled with a force torque sensor and in-house end effectors (grippers). They have the same software architecture and the facility standard EPICS-based BEAST alarm system. The MX system is compatible with SPINE bases and Unipucks. It comprises a liquid nitrogen dewar holding 384 samples (24 Unipucks) and a stay-cold gripper, and utilizes machine vision software to track the sample during operations and to calculate the final mount position on the goniometer. The bioSAXS system has an in-house engineered sample storage unit that can hold up to 360 samples (20 sample holders) which keeps samples at a user-set temperature (277 K to 300 K). The MX systems were deployed in early 2017 and the bioSAXS system in early 2019.

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425, 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493, 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015, 1741, 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5-30 keV photon energy range and delivers a flux of 4.0 × 10 12  photons s -1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12  photons s -1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods - serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25, 1362-1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ, 5, 238-246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5, 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules. Over the last few decades, most MX data have been collected at synchrotron beamlines using a large number of different detectors produced by various manufacturers and taking advantage of various protocols and goniometries. These data came in their own formats: sometimes proprietary, sometimes open. The associated metadata rarely reached the degree of completeness required for data management according to Findability, Accessibility, Interoperability and Reusability (FAIR) principles. Efforts to reuse old data by other investigators or even by the original investigators some time later were often frustrated. In the culmination of an effort dating back more than two decades, a large portion of the research community concerned with high data-rate macromolecular crystallography (HDRMX) has now agreed to an updated specification of data and metadata for diffraction images produced at synchrotron light sources and X-ray free-electron lasers (XFELs). This 'Gold Standard' will facilitate the processing of data sets independent of the facility at which they were collected and enable data archiving according to FAIR principles, with a particular focus on interoperability and reusability. This agreed standard builds on the NeXus/HDF5 NXmx application definition and the International Union of Crystallo-graphy (IUCr) imgCIF/CBF dictionary, and it is compatible with major data-processing programs and pipelines. Just as with the IUCr CBF/imgCIF standard from which it arose and to which it is tied, the NeXus/HDF5 NXmx Gold Standard application definition is intended to be applicable to all detectors used for crystallography, and all hardware and software developers in the field are encouraged to adopt and contribute to the standard., (© Herbert J. Bernstein et al. 2020.)

In macromolecular crystallography, higher flux, smaller beams, and faster detectors open the door to experiments with very large numbers of very small samples that can reveal polymorphs and dynamics but require re-engineering of approaches to the clustering of images both at synchrotrons and XFELs (X-ray free electron lasers). The need for the management of orders of magnitude more images and limitations of file systems favor a transition from simple one-file-per-image systems such as CBF to image container systems such as HDF5. This further increases the load on computers and networks and requires a re-examination of the presentation of metadata. In this paper, we discuss three important components of this problem-improved approaches to the clustering of images to better support experiments on polymorphs and dynamics, recent and upcoming changes in metadata for Eiger images, and software to rapidly validate images in the revised Eiger format., (© 2020 Author(s).)

The transformations from the primitive cells of the centered Bravais lattices to the corresponding centered cells have conventionally been listed as three-by-three matrices that transform three-space lattice vectors. Using those three-by-three matrices when working in the six-dimensional space of lattices represented as Selling scalars as used in Delone (Delaunay) reduction, one could transform to the three-space representation, apply the three-by-three matrices and then back-transform to the six-space representation, but it is much simpler to have the equivalent six-by-six matrices and apply them directly. The general form of the transformation from the three-space matrix to the corresponding matrix operating on Selling scalars (expressed in space S 6 ) is derived, and the particular S 6 matrices for the centered Delone types are listed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)., (open access.)

Algorithms for quantifying the differences between two lattices are used for Bravais lattice determination, database lookup for unit cells to select candidates for molecular replacement, and recently for clustering to group together images from serial crystallography. It is particularly desirable for the differences between lattices to be computed as a perturbation-stable metric, i.e. as distances that satisfy the triangle inequality, so that standard tree-based nearest-neighbor algorithms can be used, and for which small changes in the lattices involved produce small changes in the distances computed. A perturbation-stable metric space related to the reduction algorithm of Selling and to the Bravais lattice determination methods of Delone is described. Two ways of representing the space, as six-dimensional real vectors or equivalently as three-dimensional complex vectors, are presented and applications of these metrics are discussed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)., (open access.)

The unit-cell reduction described by Selling and used by Delone (whose early publications were under the spelling Delaunay) is explained in a simple form. The transformations needed to implement the reduction are listed. The simplicity of this reduction contrasts with the complexity of Niggli reduction.

Many problems in crystallography and other fields can be treated as nearest-neighbor problems. The neartree data structure provides a flexible way to organize and retrieve metric data. In some cases, it can provide near-optimal performance. NearTree is a software tool that constructs neartrees and provides a number of different query tools.

ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077.

Transmitting quantum information between two remote parties is a requirement for many quantum applications; however, direct transmission of states is often impossible because of noise and loss in the communication channel. Entanglement-enhanced state communication can be used to avoid this issue, but current techniques require extensive experimental resources to transmit large quantum states deterministically. To reduce these resource requirements, we use photon pairs hyperentangled in polarization and orbital angular momentum to implement superdense teleportation, which can communicate a specific class of single-photon ququarts. We achieve an average fidelity of 87.0(1)%, almost twice the classical limit of 44% with reduced experimental resources than traditional techniques. We conclude by discussing the information content of this constrained set of states and demonstrate that this set has an exponentially larger state space volume than the lower-dimensional general states with the same number of state parameters.

When coupled with transient absorption spectroscopy, pulse radiolysis, which utilizes high-energy electron pulses from an accelerator, is a powerful tool for investigating the kinetics and thermodynamics of a wide range of radiation-induced redox and electron transfer processes. The majority of these investigations detect transient species in the UV, visible, or near-IR spectral regions. Unfortunately, the often-broad and featureless absorption bands in these regions can make the definitive identification of intermediates difficult. Time-resolved vibrational spectroscopy would offer much improved structural characterization, but has received only limited application in pulse radiolysis. In this paper, we describe in detail the development of a unique nanosecond time-resolved infrared (TRIR) detection capability for condensed-phase pulse radiolysis on a new beam line at the LEAF facility of Brookhaven National Laboratory. The system makes use of a suite of high-power, continuous wave external-cavity quantum cascade lasers as the IR probe source, with coverage from 2330 to 1051 cm(-1). The response time of the TRIR detection setup is ∼40 ns, with a typical sensitivity of ∼100 μOD after 4-8 signal averages using a dual-beam probe/reference normalization detection scheme. This new detection method has enabled mechanistic investigations of a range of radiation-induced chemical processes, some of which are highlighted here.

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having "unknown function". Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.

NeXus is an effort by an international group of scientists to define a common data exchange and archival format for neutron, X-ray and muon experiments. NeXus is built on top of the scientific data format HDF5 and adds domain-specific rules for organizing data within HDF5 files, in addition to a dictionary of well defined domain-specific field names. The NeXus data format has two purposes. First, it defines a format that can serve as a container for all relevant data associated with a beamline. This is a very important use case. Second, it defines standards in the form of application definitions for the exchange of data between applications. NeXus provides structures for raw experimental data as well as for processed data.

Milk thistle (Silybum marianum) extracts are widely used as a complementary and alternative treatment of various hepatic conditions and a host of other diseases/disorders. The active constituents of milk thistle supplements are believed to be the flavonolignans contained within the extracts. In vitro studies have suggested that some milk thistle components may significantly inhibit specific cytochrome P450 (P450) enzymes. However, determining the potential for clinically significant drug interactions with milk thistle products has been complicated by inconsistencies between in vitro and in vivo study results. The aim of the present study was to determine the effect of a standardized milk thistle supplement on major P450 drug-metabolizing enzymes after a 14-day exposure period. CYP1A2, CYP2C9, CYP2D6, and CYP3A4/5 activities were measured by simultaneously administering the four probe drugs, caffeine, tolbutamide, dextromethorphan, and midazolam, to nine healthy volunteers before and after exposure to a standardized milk thistle extract given thrice daily for 14 days. The three most abundant falvonolignans found in plasma, following exposure to milk thistle extracts, were silybin A, silybin B, and isosilybin B. The concentrations of these three major constituents were individually measured in study subjects as potential perpetrators. The peak concentrations and areas under the time-concentration curves of the four probe drugs were determined with the milk thistle administration. Exposure to milk thistle extract produced no significant influence on CYP1A2, CYP2C9, CYP2D6, or CYP3A4/5 activities., (Copyright © 2014 by The American Society for Pharmacology and Experimental Therapeutics.)

Ambiguities in the article by Andrews & Bernstein [ J. Appl. Cryst. (2014), 47 , 346-359] are clarified.[This corrects the article DOI: 10.1107/S1600576713031002.].

Background: The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. The most useful/accurate strategies employed to date are based on the detection of motifs in novel structures that correspond to a specific function. Functional residues are critical components of predictively useful motifs. We have implemented a novel method, to complement current approaches, which detects motifs solely on the basis of distance restraints between catalytic residues., Results: ProMOL is a plugin for the PyMOL molecular graphics environment that can be used to create active site motifs for enzymes. A library of 181 active site motifs has been created with ProMOL, based on definitions published in the Catalytic Site Atlas (CSA). Searches with ProMOL produce better than 50% useful Enzyme Commission (EC) class suggestions for level 1 searches in EC classes 1, 4 and 5, and produce some useful results for other classes. 261 additional motifs automatically translated from Jonathan Barker's JESS motif set [Bioinformatics 19:1644-1649, 2003] and a set of NMR motifs is under development. Alignments are evaluated by visual superposition, Levenshtein distance and root-mean-square deviation (RMSD) and are reasonably consistent with related search methods., Conclusion: The ProMOL plugin for PyMOL provides ready access to template-based local alignments. Recent improvements to ProMOL, including the expanded motif library, RMSD calculations and output selection formatting, have greatly increased the program's usability and speed, and have improved the way that the results are presented.

A database of lattices using the G 6 representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction in G 6 , so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.

Niggli reduction can be viewed as a series of operations in a six-dimensional space derived from the metric tensor. An implicit embedding of the space of Niggli-reduced cells in a higher-dimensional space to facilitate calculation of distances between cells is described. This distance metric is used to create a program, BGAOL , for Bravais lattice determination. Results from BGAOL are compared with results from other metric based Bravais lattice determination algorithms. This embedding depends on understanding the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6 . This article describes an investigation of the boundary polytopes of the Niggli-reduced cone N in the six-dimensional space G 6 by algebraic analysis and organized random probing of regions near one-, two-, three-, four-, five-, six-, seven- and eightfold boundary polytope intersections. The discussion of valid boundary polytopes is limited to those avoiding the mathematically interesting but crystallographically impossible cases of zero-length cell edges. Combinations of boundary polytopes without a valid intersection in the closure of the Niggli cone or with an intersection that would force a cell edge to zero or without neighboring probe points are eliminated. In all, 216 boundary polytopes are found. There are 15 five-dimensional boundary polytopes of the full G 6 Niggli cone N .

Milk thistle (Silybum marianum) extracts, one of the most widely used dietary supplements, contain a mixture of six major flavonolignans (silybin A, silybin B, isosilybin A, isosilybin B, silychristin, and silydianin) and other components. However, the pharmacokinetics of the free individual flavonolignans have been only partially investigated in humans. Furthermore, antioxidant effects of the extract, which may underlie the basis of many therapeutic effects, have not been thoroughly assessed. The present study evaluated the pharmacokinetics of the six major flavonolignans in healthy volunteers receiving single doses of either one (175 mg), two (350 mg), or three (525 mg) milk thistle capsule(s) on three separate study visits. Additionally, the steady-state pharmacokinetic parameters were determined after the subjects were administered one capsule three times daily for 28 consecutive days. Our results demonstrated that all six flavonolignans were rapidly absorbed and eliminated. In order of abundance, the exposure to free flavonolignans was greatest for silybin A followed by silybin B, isosilybin B, isosilybin A, silychristin, and silydianin. The systemic exposure to these compounds appeared linear and dose proportional. The disposition of flavonolignans was stereoselective, as evidenced by the apparent clearance of silybin B, which was significantly greater than silybin A, whereas the apparent clearance of isosilybin B was significantly lower than isosilybin A. The concentrations of urinary 8-epi-prostaglandin F2α, a commonly used biomarker of oxidative status in humans, were considerably decreased in study subjects after a 28-day exposure to the extract (1.3 ± 0.9 versus 0.8 ± 0.9 ng/mg creatinine) but failed to reach statistical significance (P = 0.076).

The aim of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is to allow users who are experts in one scripting language to use that language in a second molecular visualization environment without requiring the user to learn a new scripting language. ConSCRIPT, the first SBEVSL release, is a plug-in for PyMOL that accepts RasMol scripting commands either as premade scripts or as line-by-line entries from PyMOL's own command line. The plug-in is available for download at http://sourceforge.net/projects/sbevsl/files in the ConSCRIPT folder. Biochemistry and Molecular Biology Education Vol. 38, No. 6, pp. 419-422, 2010., (Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.)

The PGALRS (pseudo-Gaussian approximation to Lee-Richards surfaces) algorithm is discussed. By modeling electron density with unphysical pseudo-Gaussian atoms, the Lee-Richards surface can be approximated by a contour level of that density in time approximately linear in the number of atoms. Having that contour level, the atoms and residues closest to that surface can be identified in average time O[n(2/3)log(n)] using a NearTree-based nearest neighbor search. If a high-quality Lee-Richards surface is required, then, as a final stage, one of the standard Lee-Richards algorithms can be used but considering only the previously identified surface residues; the typical cost is thereby reduced to O[n(2/3)log(n)], making the overall average time for all the steps O(n). For very large macromolecules, such a reduction in computational burden may be essential to being able to render a meaningful molecular surface. This approach extends the feasible range of application for existing molecular surface software, such as MSMS, to larger macromolecules, especially to macromolecules with more than 50 000 atoms, and can be used as a starting point for surface-based (as opposed to backbone-based) motif identification, e.g. using ProMol.

Objective: To compare the memory effects of continuation electroconvulsive therapy (C-ECT) versus continuation pharmacologic intervention (C-PHARM) at 12 and 24 weeks after completion of acute electroconvulsive therapy (ECT)., Method: Eighty-five patients with Structured Clinical Interview for DSM-IV-diagnosed unipolar major depressive disorder, enrolled in a multisite, randomized, parallel-design trial conducted at 5 academic medical centers from 1997 to 2004, who had remitted with an acute course of bilateral ECT and remained unrelapsed through 24 weeks of continuation therapy, were included in this analysis. They were randomly assigned to C-ECT (10 treatments) or nortriptyline plus lithium (monitored by serum blood levels) for 24 weeks. Objective neuropsychological measures of retrograde and anterograde memory and subjective assessment of memory were obtained at baseline, 12 weeks, and 24 weeks. The Rey Auditory-Verbal Learning Test and the Autobiographical Memory Interview were the primary outcome measures., Results: The C-PHARM group showed a greater group difference (P < .01) for baseline to 12-week change for the Autobiographical Memory Interview. No other memory measures showed group differences for change scores from baseline to 12 weeks. Groups showed no baseline to 24-week change-score differences on any of the memory measures. For both groups, 12-week objective anterograde memory scores (eg, Auditory-Verbal Learning Test percent retention P = .0001; Rey-Osterrieth Complex Figure or Taylor Figure percent retention P < .002) and 24-week subjective memory scores were significantly improved (Squire Subjective Memory Questionnaire P < .02) over baseline. This result reflects the apparent resolution of a presumed decrement in anterograde memory associated with acute ECT preceding this study., Conclusions: The finding of no memory outcome differences between unrelapsed recipients of C-ECT and C-PHARM is consistent with clinical experience. Memory effects have only a small role in the choice between C-ECT and C-PHARM., (Copyright 2010 Physicians Postgraduate Press, Inc.)

Background: Although electroconvulsive therapy (ECT) has been shown to be extremely effective for the acute treatment of major depression, it has never been systematically assessed as a strategy for relapse prevention., Objective: To evaluate the comparative efficacy of continuation ECT (C-ECT) and the combination of lithium carbonate plus nortriptyline hydrochloride (C-Pharm) in the prevention of depressive relapse., Design: Multisite, randomized, parallel design, 6-month trial performed from 1997 to 2004., Setting: Five academic medical centers and their outpatient psychiatry clinics., Patients: Two hundred one patients with Structured Clinical Interview for DSM-IV-diagnosed unipolar depression who had remitted with a course of bilateral ECT., Interventions: Random assignment to 2 treatment groups receiving either C-ECT (10 treatments) or C-Pharm for 6 months., Main Outcome Measure: Relapse of depression, compared between the C-ECT and C-Pharm groups., Results: In the C-ECT group, 37.1% experienced disease relapse, 46.1% continued to have disease remission at the study end, and 16.8% dropped out of the study. In the C-Pharm group, 31.6% experienced disease relapse, 46.3% continued to have disease remission, and 22.1% dropped out of the study. Both Kaplan-Meier and Cox proportional hazards regression analyses indicated no statistically significant differences in overall survival curves and time to relapse for the groups. Mean +/- SD time to relapse for the C-ECT group was 9.1 +/- 7.0 weeks compared with 6.7 +/- 4.6 weeks for the C-Pharm group (P = .13). Both groups had relapse proportions significantly lower than a historical placebo control from a similarly designed study., Conclusions: Both C-ECT and C-Pharm were shown to be superior to a historical placebo control, but both had limited efficacy, with more than half of patients either experiencing disease relapse or dropping out of the study. Even more effective strategies for relapse prevention in mood disorders are urgently needed.

Patients treated with electroconvulsive therapy (ECT) were divided into those with less severe depression and those with more severe depression. In the less severely depressed group, high somatic anxiety and hypochondriasis predicted a low likelihood of sustained remission with ECT. In the more severely depressed group, these traits were not predictive of ECT outcome.

Background: Remission of illness in patients with major depressive disorder (MDD) is achieved in less than half of patients initially treated with medication. Electroconvulsive therapy (ECT) is another treatment option. We report the speed of response and remission rates in a cohort of depressed patients who received a course of acute-phase ECT in the initial phase of an ongoing multicenter randomized trial of continuation ECT versus pharmacotherapy., Method: Patients with MDD according to DSM-IV criteria received bilateral ECT 3 times weekly. Prior to each treatment, a 24-item Hamilton Rating Scale for Depression (HAM-D-24) score was obtained by a clinical rater. Sustained response was defined as a > or = 50% reduction in baseline HAM-D-24 score for at least 2 and all subsequent measurement occasions. Remission was defined as HAM-D-24 scores of < or = 10 for at least the last 2 consecutive assessments. Data were collected from May 1997 through November 2000., Results: Of the 253 patients who entered the study, 86% (N = 217) completed the acute course of ECT. Sustained response occurred in 79% of the sample, and remission occurred in 75% of the sample (N = 253); 34% (85/253) of patients achieved remission at or before ECT #6 (week 2), and 65% (164/253) achieved remission at or before ECT #10 (weeks 3-4). Over half (54%; 136/253) had an initial first response by ECT #3 (end of week 1)., Conclusion: ECT was associated with rapid response and remission in a high percentage of patients. ECT warrants early consideration in treatment algorithms for patients with MDD.

Objective: To compare the relative efficacy of electroconvulsive therapy (ECT) in psychotic and nonpsychotic patients with unipolar major depression., Methods: The outcome of an acute ECT course in 253 patients with nonpsychotic (n = 176) and psychotic (n = 77) unipolar major depression was assessed in the first phase of an ongoing National Institute of Mental Health-supported four-hospital collaborative study of continuation treatments after successful ECT courses. ECT was administered with bilateral electrode placement at 50% above the titrated seizure threshold. The remission criteria were rigorous: a score