bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ligand Dynamics in the Solid: Lithium‐fluorenide and Lithium‐benzo[b]fluorenide N,N,N′,N′‐Tetramethylethylenediamine (tmeda) Complexes
Authors: Focke Arnd , Hausmann Heike , Jost Steffen , Günther Harald 
Published: December 2012

AbstractThe dynamic behavior of the N,N,N′,N′‐tetramethylethylenediamine (tmeda) ligand has been studied in solid lithium‐fluorenide(tmeda) (3) and lithium‐benzo[b]fluorenide(tmeda) (4) using CP/MAS solid‐state 13C‐ and 15N‐NMR spectroscopy. It is shown that, in the ground state, the tmeda ligand is oriented parallel to the long molecular axis of the fluorenide and benzo[b]fluorenide systems. At low temperature (<250 K), the 13C‐NMR spectrum exhibits two MeN signals. A dynamic process, assigned to a 180° rotation of the five‐membered metallacycle (π‐flip), leads at elevated temperatures to coalescence of these signals. Line‐shape calculations yield ΔH‡=42.7 kJ mol−1, ΔS‡=−5.3 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=44.3 kJ mol−1 for 3, and ΔH‡=36.8 kJ mol−1, ΔS‡=−17.7 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=42.1 kJ mol−1 for 4, respectively. A second dynamic process, assigned to ring inversion of the tmeda ligand, was detected from the temperature dependence of T1ρ, the 13C spin‐lattice relaxation time in the rotating frame, and led to ΔH‡=24.8 kJ mol−1, ΔS‡=−49.2 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=39.5 kJ mol−1 for 3, and ΔH‡=18.2 kJ mol−1, ΔS‡=−65.3 J mol−1 K−1, and $\rm{\Delta G_{298}^{\ddag}}$=37.7 kJ mol−1 for 4, respectively. For (D12)‐3, the rotation of the CD3 groups has also been studied, and a barrier Ea of 14.1 kJ mol−1 was found.
Lewis Acid‐Mediated Addition of Amino Acid‐Substituted α‐Allylsilanes to Aromatic Acetals
Authors: Brook Michael A. , Mohamed Mustafa 
Published: December 2012

AbstractUnnatural amino acids extend the pharmacological formulator's toolkit. Strategies to prepare unnatural amino acid derivatives using Lewis acid‐activated allylsilane reactions are few. In this regard, we examined the utility of allylsilanes bearing an amino acid substituent in the reaction. Diastereoselective addition of methyl 2‐(N‐PG‐amino)‐3‐(trimethylsilyl)pent‐4‐enoate and methyl (E)‐2‐(N‐PG‐amino)‐3‐(trimethylsilyl)hex‐4‐enoate (PG=protecting group), 2 and 13, respectively, to aromatic acetals in the presence of Lewis acids is described. Of those examined, TiCl4 was found to be the most effective Lewis acid for promoting the addition. At least 1 equiv. of TiCl4 was required to achieve high yields, whereas 2 equiv. of BF3⋅OEt2 were required for comparable outcomes. Excellent selectivity (>99% syn/anti) and high yield (up to 89%) were obtained with halo‐substituted aromatic acetals, while more electron‐rich electrophiles led to both lower yields and diastereoselectivities.
Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β‐Peptide Molecules
Authors: Wang Dongqi , Freitag Fabian , Gattin Zrinka , Haberkern Hannah , Jaun Bernhard , Siwko Magdalena , Vyas Rounak , van Gunsteren Wilfred F. , Dolenc Jožica 
Published: December 2012

AbstractA molecular‐dynamics (MD) simulation study of two heptapeptides containing α‐ and β‐amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β‐hairpin‐like conformations, while peptide 8 adopts a 14/15‐helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atomatom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and 3J‐coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/β‐peptides in MeOH.
Free flap reconstruction of oral composite defect complicated by intraoperative cardiac arrest: A case report
Authors: Young Lindsay , Myers Larry L. 
Published: December 2012

AbstractWe report the case of intraoperative cardiac arrest of a patient undergoing free tissue harvest for an oral composite defect and subsequent completion of reconstruction with simultaneous double flaps. A 54‐year‐old man with advanced carcinoma of the tongue underwent near‐total glossectomy, segmental mandiblectomy, and bilateral neck dissections. We planned a fasciocutaneous anterolateral thigh flap to reconstruct the glossectomy defect, and a fibula osteocutaneous flap for the mandible defect. After the fibula flap harvest, the patient suffered a cardiac arrest. After a 4‐min code, the patient regained a sinus rhythm and became hemodynamically stable. We completed the cancer resection and banked the pedicled, osteotomized fibula flap in the lower extremity. We took the patient back to the operating room on postoperative day number 5 for successful reconstruction with simultaneous fibula and ALF flaps. The microvascular surgeon must always be poised to rapidly address intraoperative complications that may critically compromise the success of the free flap or, more seriously, jeopardize the patient's life. © 2012 Wiley Periodicals, Inc. Microsurgery, 2013.
Genetic Counselors’ Current Use of Personal Health Records‐Based Family Histories in Genetic Clinics and Considerations for Their Future Adoption
Authors: Widmer Chaney , DeShazo Jonathan P. , Bodurtha Joann , Quillin John , Creswick Heather 
Published: December 2012

AbstractGiven the widespread adoption of electronic medical records and recent emergence of electronic family history tools, we examined genetic counselors’ perspectives on the emerging technology of the personal health record (PHR)‐based family history tool that links to an electronic medical record (EMR). Two‐hundred thirty‐three genetic counselors responded to an on‐line survey eliciting current use of electronic family history (EFH) tools and familiarity with PHR‐based family history tools. Additionally, after being shown a series of screen shots of a newly developed PHR‐based family history tool based on the U.S. Surgeon General's My Family Health Portrait (United States Department of Health and Human Services 2009), participants were surveyed about the perceived usefulness, ease of use, and impact on current workflow that this kind of tool would have in their practices. Eighty‐three percent reported that their institution has an EMR, yet only 35 % have a dedicated space for family history. Eighty‐two percent reported that less than 5 % of their patients have a PHR, and only 16 % have worked with patients who have a PHR. Seventy‐two percent or more agreed that a PHR‐based family history tool would facilitate communication, increase accuracy of information, ensure consistency in recording information, increase focus on actual counseling, reduce repetitive questions, improve efficiency, and increase the legibility and clarity. Our findings suggest that participants were familiar with existing EFH tools, but that the majority did not use them in practice. Genetic counselors’ adoption of such tools is limited due to non‐existence of this kind of technology or inability to integrate it into their clinics. They are also strongly in favor of adopting a PHR‐based family history tool in genetics clinics, but have practical concerns that must be addressed before the tool can be implemented.
Ordinary women and men: superintendents and Jews in the Budapest yellow-star houses in 1944–1945
Authors: RIGÓ MÁTÉ 
Published: December 2012

ABSTRACT:The present article investigates how everyday people shaped the outcome of discriminatory measures during the Nazi persecution of Budapest Jews, primarily by looking into micro-level social interactions between superintendents and confined Jews during ghettoization in the Hungarian capital (1944). I argue that besides a multiplicity of relevant political, social and military reasons determining the fate of Budapest Jews, the urban specificity of the Holocaust also needs to be taken into account, given that location and access to urban space enabled different personal strategies to contest or aggravate anti-Semitic persecution. Especially older, nineteenth-century apartment buildings fostered the autonomy of superintendents, who could act independently of various authorities, exploiting certain Jews while aiding others. The article demonstrates how many superintendents made use of this power effectively as the successive regimes toughened their anti-Semitic policies. In addition, the investigation of individual motives and the micro levels of segregation and discrimination highlight major differences between and within apartment buildings, despite the supposedly homogeneous discrimination against Jews envisaged by Nazi policy makers.
Violence, Nonviolence, and the Palestinian National Movement. By Wendy Pearlman
Authors: Nepstad Sharon Erickson 
Published: December 2012

Violence, Nonviolence, and the Palestinian National Movement. By Wendy Pearlman. New York: Cambridge University Press, 2011. 304p. $99.00.In recent years, social scientific research on nonviolent resistance has burgeoned. Yet many studies focus on the factors associated with nonviolent movements' success or failure. In her book, Wendy Pearlman poses different questions. Instead of asking when and how nonviolence works, she asks why some activists choose nonviolent tactics while others choose violent ones. Additionally, she asks why movements may, over time, shift between armed and unarmed strategies.
Neoliberalism, Race, and the American Welfare State
Authors: Mead Lawrence M. 
Published: December 2012

Disciplining the Poor: Neoliberal Paternalism and the Persistent Power of Race.By Joe Soss, Richard C. Fording, and Sanford F. Schram. Chicago: University of Chicago Press, 2011. 368p. $75.00 cloth, $25.00 paper.It is more than 15 years since the Personal Responsibility and Work Opportunity Act was passed in 1996, famously described by then-President Bill Clinton as “the end of welfare as we know it.” InDisciplining the Poor, Joe Soss, Richard Fording, and Sanford Schram analyze recent changes in US welfare policy as reflections of broader transformations of the “governance” of poverty, arguing that these transformations represent a new form of “neoliberal paternalism” in which race continues to be an important element. In this symposium, a diverse group of political scientists working on welfare issues have been asked to critically assess the book's account and to comment more broadly on the importance of the “governance of poverty” to the future of American politics.—Jeffrey C. Isaac, Editor
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
Authors: Zaretzki Jed , Bergeron Charles , Huang Tao-wei , Rydberg Patrik , Swamidass S. Joshua , Breneman Curt M. 
Published: December 2012

Abstract
Summary: Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules. Predictions may be made for the promiscuous 2C9, 2D6 and 3A4 CYP isozymes, as well as CYPs 1A2, 2A6, 2B6, 2C8, 2C19 and 2E1. RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes. Server execution time is fast, taking on average 2s to encode a submitted molecule and 1s to apply a given model, allowing for high-throughput use in lead optimization projects.
Availability: RS-WebPredictor is accessible for free use at http://reccr.chem.rpi.edu/Software/RS-WebPredictor/
Contact: brenec@rpi.edu
Fast and robust optical flow for time-lapse microscopy using super-voxels
Authors: Amat Fernando , Myers Eugene W. , Keller Philipp J. 
Published: December 2012

Abstract
Motivation: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data.
Results: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions.
Availability: Source code freely available in the Software section at http://janelia.org/lab/keller-lab.
Contact: amatf@janelia.hhmi.org or kellerp@janelia.hhmi.org
Supplementary information: Supplementary data are available at Bioinformatics online.
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
Authors: Albanese Davide , Filosi Michele , Visintainer Roberto , Riccadonna Samantha , Jurman Giuseppe , Furlanello Cesare 
Published: December 2012

Abstract
Summary: We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large ( = 1340) microarray and Illumina GAII RNA-seq transcriptomics datasets.
Availability and implementation: Source code and binaries are freely available for download under GPL3 licence at http://minepy.sourceforge.net for minepy and through the CRAN repository http://cran.r-project.org for the R package minerva. All software is multiplatform (MS Windows, Linux and OSX).
Contact: furlan@fbk.eu
Supplementary information: Supplementary data are available at Bioinformatics online.
Sharing the Northeast Atlantic mackerel
Authors: Hannesson Rögnvaldur 
Published: December 2012

AbstractThe sharing of the Northeast Atlantic mackerel (Scomber scombrus) stock is analysed as a game between four parties: the European Union, Norway, the Faroe Islands, and Iceland. Consideration is given to how the outcome depends on the nature of the stock's migrations. Two types of migrations are considered: (i) density-dependent, where the mackerel migrates into the Icelandic economic zone only if it exceeds 3.5 million t, and (ii) stochastic migrations, where the said migrations are stochastic. It is determined that the Faroe Islands would never accept a cooperative solution wherein they can only fish with the globally optimal fishing mortality within their own zone. This is also true for Iceland when the migrations into her zone are stochastic, but not if they are density-dependent. In the latter case, the other players have incentives to retaliate to Icelandic overfishing by fishing harder, which greatly reduces the number of years when mackerel are available in the Icelandic zone. It is assumed that the objective is maximization of the catch volume over a time-horizon of 50 years.
Transcriptional and Functional Classification of the GOLVEN/ROOT GROWTH FACTOR/CLE-Like Signaling Peptides Reveals Their Role in Lateral Root and Hair Formation
Authors: Fernandez Ana , Drozdzecki Andrzej , Hoogewijs Kurt , Nguyen Anh , Beeckman Tom , Madder Annemieke , Hilson Pierre 
Published: December 2012

AbstractThe GOLVEN (GLV)/ROOT GROWTH FACTORS/CLE-Like small signaling peptide family is encoded by 11 genes in Arabidopsis (Arabidopsis thaliana). Some of them have already been shown to control root meristem maintenance, auxin fluxes, and gravitropic responses. As a basis for the detailed analysis of their function, we determined the expression domains for each of the 11 GLV genes with promoter-reporter lines. Although they are collectively active in all examined plant parts, GLV genes have highly specific transcription patterns, generally restricted to very few cells or cell types in the root and shoot and in vegetative and reproductive tissues. GLV functions were further investigated with the comparative analysis of root phenotypes induced by gain- and loss-of-function mutants or in treatments with GLV-derived synthetic peptides. We identified functional classes that relate to the gene expression domains in the primary root and suggest that different GLV signals trigger distinct downstream pathways. Interestingly, GLV genes transcribed at the early stages of lateral root development strongly inhibited root branching when overexpressed. Furthermore, transcription patterns together with mutant phenotypes pointed to the involvement of GLV4 and GLV8 in root hair formation. Overall, our data suggest that nine GLV genes form three subgroups according to their expression and function within the root and offer a comprehensive framework to study the role of the GLV signaling peptides in plant development.
PYRABACTIN RESISTANCE1-LIKE8 Plays an Important Role for the Regulation of Abscisic Acid Signaling in Root
Authors: Antoni Regina , Gonzalez-Guzman Miguel , Rodriguez Lesia , Peirats-Llobet Marta , Pizzio Gaston A. , Fernandez Maria A. , De Winne Nancy , De Jaeger Geert , Dietrich Daniela , Bennett Malcom J. , Rodriguez Pedro L. 
Published: December 2012

AbstractAbscisic acid (ABA) signaling plays a critical role in regulating root growth and root system architecture. ABA-mediated growth promotion and root tropic response under water stress are key responses for plant survival under limiting water conditions. In this work, we have explored the role of Arabidopsis (Arabidopsis thaliana) PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS for root ABA signaling. As a result, we discovered that PYL8 plays a nonredundant role for the regulation of root ABA sensitivity. Unexpectedly, given the multigenic nature and partial functional redundancy observed in the PYR/PYL family, the single pyl8 mutant showed reduced sensitivity to ABA-mediated root growth inhibition. This effect was due to the lack of PYL8-mediated inhibition of several clade A phosphatases type 2C (PP2Cs), since PYL8 interacted in vivo with at least five PP2Cs, namely HYPERSENSITIVE TO ABA1 (HAB1), HAB2, ABA-INSENSITIVE1 (ABI1), ABI2, and PP2CA/ABA-HYPERSENSITIVE GERMINATION3 as revealed by tandem affinity purification and mass spectrometry proteomic approaches. We also discovered that PYR/PYL receptors and clade A PP2Cs are crucial for the hydrotropic response that takes place to guide root growth far from regions with low water potential. Thus, an ABA-hypersensitive pp2c quadruple mutant showed enhanced hydrotropism, whereas an ABA-insensitive sextuple pyr/pyl mutant showed reduced hydrotropic response, indicating that ABA-dependent inhibition of PP2Cs by PYR/PYLs is required for the proper perception of a moisture gradient.
LnIs a Key Regulator of Leaflet Shape and Number of Seeds per Pod in Soybean
Authors: Jeong Namhee , Suh Su Jeoung , Kim Min-Hee , Lee Seukki , Moon Jung-Kyung , Kim Hong Sig , Jeong Soon-Chun 
Published: December 2012

AbstractNarrow leaflet soybean (Glycine max) varieties tend to have more seeds per pod than broad leaflet varieties. Narrow leaflet in soybean is conferred by a single recessive gene, ln. Here, we show that the transition from broad (Ln) to narrow leaflet (ln) is associated with an amino acid substitution in the EAR motif encoded by a gene (designated Gm-JAGGED1) homologous to Arabidopsis JAGGED (JAG) that regulates lateral organ development and the variant exerts a pleiotropic effect on fruit patterning. The genomic region that regulates both the traits was mapped to a 12.6-kb region containing only one gene, Gm-JAG1. Introducing the Gm-JAG1 allele into a loss-of-function Arabidopsis jagged mutant partially restored the wild-type JAG phenotypes, including leaf shape, flower opening, and fruit shape, but the Gm-jag1 (ln) and EAR-deleted Gm-JAG1 alleles in the jagged mutant did not result in an apparent phenotypic change. These observations indicate that despite some degree of functional change of Gm-JAG1 due to the divergence from Arabidopsis JAG, Gm-JAG1 complemented the functions of JAG in Arabidopsis thaliana. However, the Gm-JAG1 homoeolog, Gm-JAG2, appears to be sub- or neofunctionalized, as revealed by the differential expression of the two genes in multiple plant tissues, a complementation test, and an allelic analysis at both loci.
Relocalization of Late Blight Resistance Protein R3a to Endosomal Compartments Is Associated with Effector Recognition and Required for the Immune Response
Authors: Engelhardt Stefan , Boevink Petra C. , Armstrong Miles R. , Ramos Maria Brisa , Hein Ingo , Birch Paul R.J. 
Published: December 2012

Abstract
An important objective of plant–pathogen interactions research is to determine where resistance proteins detect pathogen effectors to mount an immune response. Many nucleotide binding–Leucine-rich repeat (NB-LRR) resistance proteins accumulate in the plant nucleus following effector recognition, where they initiate the hypersensitive response (HR). Here, we show that potato (Solanum tuberosum) resistance protein R3a relocates from the cytoplasm to endosomal compartments only when coexpressed with recognized Phytophthora infestans effector form AVR3aKI and not unrecognized form AVR3aEM. Moreover, AVR3aKI, but not AVR3aEM, is also relocalized to endosomes in the presence of R3a. Both R3a and AVR3aKI colocalized in close physical proximity at endosomes in planta. Treatment with brefeldin A (BFA) or wortmannin, inhibitors of the endocytic cycle, attenuated both the relocalization of R3a to endosomes and the R3a-mediated HR. No such effect of these inhibitors was observed on HRs triggered by the gene-for-gene pairs Rx1/PVX-CP and Sto1/IpiO1. An R3a(D501V) autoactive MHD mutant, which triggered HR in the absence of AVR3aKI, failed to localize to endosomes. Moreover, BFA and wortmannin did not alter cell death triggered by this mutant. We conclude that effector recognition and consequent HR signaling by NB-LRR resistance protein R3a require its relocalization to vesicles in the endocytic pathway.