bluuebunny/crossref_metadata_2025_split huggingface dataset:
Employing ProteoWizard to Convert Raw Mass Spectrometry Data
Authors: Holman Jerry D. , Tabb David L. , Mallick Parag 
Published: June 2014

AbstractAfter raw data have been captured by mass spectrometers in biological LC‐MS/MS experiments, they must be converted from vendor‐specific binary files to open‐format files for manipulation by most software. This protocol details the use of ProteoWizard software for this conversion, taking format features, coding options, and vendor particularities into account. This protocol will aid researchers in preparing their data for analysis by database search engines and other bioinformatics tools. Curr. Protoc. Bioinform. 46:13.24.1‐13.24.9. © 2014 by John Wiley & Sons, Inc.
Buildup of a dynamically supported orogenic plateau: Numerical modeling of the Zagros/Central Iran case study
Authors: François T. , Burov E. , Agard P. , Meyer B. 
Published: June 2014

AbstractThe Iranian plateau is a vast inland region with a smooth average elevation of c. 1.5 km formed at the rear of the Zagros orogen as a result of the Arabia‐Eurasia collision (i.e., over the last 30–35 Myr). This collision zone is of particular interest due to its disputed resemblance to the faster Himalayan collision, which gave birth to the Tibetan plateau around 50 Myr ago. Recent studies have suggested that a recent (10–5 Ma) slab break‐off event below Central Iran caused the formation of the Iranian plateau. Here, we test several hypotheses through large‐scale (3082 × 590 km) numerical models of continental subduction models that incorporate a free upper surface erosion, rheological stratification, brittle‐elastic‐ductile rheologies, and metamorphic phase changes (density and physical properties) and account for the specific crustal and thermal structure of the Arabian and Iranian continental lithospheres. We test the impact of the transition from oceanic to continental subduction and the topographic consequences of the progressive slowdown of the convergence rate during continental subduction. Our results demonstrate the role of mantle flow beneath the overriding plate, initiated as an indirect consequence of slab break‐off. This flow creates a dynamic topography support during continental subduction and results in delamination of the overriding plate lithospheric mantle followed by isostatic readjustment, hence of further uplift and maintenance of a plateau‐like topography without significant crustal thickening. The slowdown of the convergence rate during the development of the continental subduction/collision phase largely contributes to this process by controlling the timing and depth of slab break‐off.
Mechanical analysis of a natural example of onland gravity gliding: The role of river incision and deposition
Authors: Messager Grégoire , Hassani Riad , Nivière Bertrand 
Published: June 2014

AbstractGravity gliding implies rigid translation of a body down a slope where displacements are parallel to a tilted detachment plane. Although large‐scale gravity gliding is commonly observed offshore, under conditions of high fluid overpressure and abundant upslope sedimentary supply, its occurrence on land is debated. We investigate the mechanical feasibility of such a process as well as the role of fluvial incision and sedimentation down the slope in the initiation of the gliding. We use a two‐dimensional (2‐D) finite element model combined with a 2‐D failure analysis approach. The numerical models simulate the deformation and provide quantitative estimates of the failure criteria at the head and toe of the overburden. Analytical solutions approximate the numerical results by taking into account the fluvial incision and sedimentation, the internal friction angle, and the thickness and length of the overburden. Our models are based on a field example in the Andean foothills of Argentina, where gravity gliding of a 1000 m thick section is suspected above a crustal‐scale anticline. The incision and sedimentation reduce and strengthen, respectively, the downslope resistance to contractional failure. The critical slope at which the gliding is initiated is reduced by fluvial incision and increased by sedimentation. We show that tectonic uplift may lead to large‐scale gravity gliding on land where the overburden thickness is less than 2000 m. Incision facilitates and localizes the frontal shortening. Incision greater than 1000 m may trigger gliding for overburden up to 4000 m thick, while sedimentation thicker than 1000 m inhibits gliding. These results show that thin‐skinned onland gravity gliding could be common in tectonically active regions where incision is important.
Experimental study of the interplay between magmatic rift intrusion and flank instability with application to the 2001 Mount Etna eruption
Authors: Le Corvec Nicolas , Walter Thomas R. , Ruch Joel , Bonforte Alessandro , Puglisi Giuseppe 
Published: June 2014

AbstractMount Etna volcano is subject to transient magmatic intrusions and flank movement. The east flank of the edifice, in particular, is moving eastward and is dissected by the Timpe Fault System. The relationship of this eastward motion with intrusions and tectonic fault motion, however, remains poorly constrained. Here we explore this relationship by using analogue experiments that are designed to simulate magmatic rift intrusion, flank movement, and fault activity before, during, and after a magmatic intrusion episode. Using particle image velocimetry allows for a precise temporal and spatial analysis of the development and activity of fault systems. The results show that the occurrence of rift intrusion episodes has a direct effect on fault activity. In such a situation, fault activity may occur or may be hindered, depending on the interplay of fault displacement and flank acceleration in response to dike intrusion. Our results demonstrate that a complex interplay may exist between an active tectonic fault system and magmatically induced flank instability. Episodes of magmatic intrusion change the intensity pattern of horizontal flank displacements and may hinder or activate associated faults. We further compare our results with the GPS data of the Mount Etna 2001 eruption and intrusion. We find that syneruptive displacement rates at the Timpe Fault System have differed from the preeruptive or posteruptive periods, which shows a good agreement of both the experimental and the GPS data. Therefore, understanding the flank instability and flank stability at Mount Etna requires consideration of both tectonic and magmatic forcing.
ENU Mutagenesis in the Mouse
Authors: Stottmann Rolf , Beier David 
Published: June 2014

AbstractThis article describes the treatment of laboratory mice with the mutagen N‐ethyl‐N‐nitrosourea (ENU) to induce very highly increased rates of mutation throughout the genome. Further, it describes several popular mating schemes designed to produce animals displaying phenotypes associated with the induced mutations. Curr. Protoc. Mouse Biol. 4:25‐35 © 2014 by John Wiley & Sons, Inc.
In Vitro Fertilization in Mice Using the MBCD‐GSH Protocol
Authors: Guan Mo , Bogani Debora , Marschall Susan , Raspa Marcello , Takeo Toru , Nakagata Naomi , Fray Martin 
Published: June 2014

AbstractHistorically, timed mating of either naturally cycling or superovulated females has been the mainstay of pre‐implantation embryo production. However, rising cage costs and the rapid expansion of biomedical research programs has necessitated the development of high‐throughput approaches to mouse embryo production. In vitro fertilization (IVF) represents one such versatile tool offering many advantages to busy mouse facilities in terms of efficient use of space and resources. For example, strains can be taken off the shelf, frozen quickly as sperm, and recovered at a later date, small colonies can be rapidly expanded to meet demand, and IVF can be used to rescue strains that fail to breed or where the founder male is ill or has died suddenly. This article describes an IVF protocol currently used by many reproductive technologists to assist mouse biology programs. Curr. Protoc. Mouse Biol. 4:67‐83 © 2014 by John Wiley & Sons, Inc.
Systematic Investigation of the Ring‐Expansion Reaction of N‐Heterocyclic Carbenes with an Iminoborane Dihydride
Authors: Franz Daniel , Inoue Shigeyoshi 
Published: June 2014

AbstractConversions of iminoboranes with an N‐heterocyclic carbene (NHC) result in borane dihydride formation (BDF) concomitant with dihydrogenated NHC. The iminoborane dihydrides are prone to a hydride‐mediated ring‐expansion reaction (RER) at elevated temperature, that is, the insertion of the boron atom into the adjacent CN bond of the NHC to yield boracycles. Upon conversion of a saturated‐backbone NHC with respective iminoborane precursors RER yet occurs at ambient temperature to yield the ring‐expanded products. When a less bulky iminoborane is brought in contact with sterically unhindered NHC neither the iminoborane dihydride is stable at room temperature nor is the RER observed to take place upon heating. The conversions of iminoboranes with very bulky NHC do not show BDF at ambient temperature and only in the case of the less hindered borane precursor the RER is found to proceed in a controlled fashion upon heating.
Optimization of headways with stop‐skipping control: a case study of bus rapid transit system
Authors: Chen Xumei , Hellinga Bruce , Chang Chengzhi , Fu Liping 
Published: June 2014

SummaryBus rapid transit system is designed to provide high‐quality and cost‐efficient passenger transportation services. In order to achieve this design objective, effective scheduling strategies are required. This research aims at improving the operation efficiency and service quality of a BRT system through integrated optimization of its service headways and stop‐skipping strategy. Based on cost analysis for both passengers and operation agencies, an optimization model is established. A genetic algorithms based algorithm and an application‐oriented solution method are developed. Beijing BRT Line 2 has been chosen as a case study, and the effectiveness of the optimal headways with stop‐skipping services under different demand levels has been analyzed. The results has shown that, at a certain demand level, the proposed operating strategy can be most advantageous for passengers with an accepted increase of operating costs, under which the optimum headway is between 3.5 and 5.5 min for stop‐skipping services during the morning peak hour depending on the demand with the provision of stop‐skipping services. The effectiveness of the optimal headways with stop‐skipping services is compared with those of existing headways and optimal headways without stop‐skipping services. The results show that operating strategies under the optimal headways with stop‐skipping services outperforms the other two operating strategies with respect to total costs and in‐vehicle time for passengers. Copyright © 2014 John Wiley & Sons, Ltd.
Statin use and its effect on all‐cause mortality of melanoma patients: a population‐based Dutch cohort study
Authors: Livingstone Elisabeth , Hollestein Loes M. , van Herk‐Sukel Myrthe P. P. , van de Poll‐Franse Lonneke , Joosse Arjen , Schilling Bastian , Nijsten Tamar , Schadendorf Dirk , de Vries Esther 
Published: June 2014

AbstractPreclinical data showed anticancer effects of statins in melanoma, but meta‐analyses could not demonstrate a reduced melanoma incidence in statin users. Rather than preventing occurrence, statins might reduce growth and metastatic spread of melanomas and ultimately improve survival. In this population‐based study, we investigated the relationship between statin use and survival of melanoma patients. Patients ≥18 years who were diagnosed with cutaneous melanoma (Breslow thickness >1 mm) and registered in the Eindhoven Cancer Registry and in PHARMO Database Network between 1 January 1998 and 31 December 2010 were eligible. The hazard ratio (HR) of all‐cause mortality was calculated by employing adjusted time‐dependent and time‐fixed Cox proportional hazard models. Disease‐specific survival was estimated by means of 3‐year relative survival rates (RSR). A control cohort of randomly selected patients using statins from PHARMO Database Network matched on age and gender was used to compare RSR of statin users to the general population. After melanoma diagnosis, 171 of 709 patients used statins. Use of statins showed a nonsignificantly decreased hazard of death (adjusted HR 0.76, 95% confidence interval [CI] 0.50–1.61). After stratification for gender, male but not female statin users showed a favorable outcome compared to nonusers (HR 0.57, 95% CI 0.32–0.99; HR 1.22, 95% CI 0.62–2.38, respectively). Three‐year RSR for male statin users tended to be higher than for nonusers (91% vs. 80.5%, P = 0.06), no differences were observed in women (87.1% vs. 92.5%, P = 0.76). Statin use was not associated with an improved survival of melanoma patients. The trend for better survival of male in contrast to female statin users warrants further research.
Tuning the Electronic Coupling in Cyclometalated Diruthenium Complexes through Substituent Effects: A Correlation between the Experimental and Calculated Results
Authors: Shao Jiang‐Yang , Zhong Yu‐Wu 
Published: June 2014

AbstractA common bridging ligand, 3,3′,5,5′‐tetrakis(N‐methylbenzimidazol‐2‐yl)biphenyl, and four terpyridine terminal ligands with various substituents (amine, tolyl, nitro, and ester groups) have been used to synthesize ten cyclometalated diruthenium complexes 12+–102+. Among them, compounds 12+–62+ are redox nonsymmetric, and others are symmetric. These complexes show two RuIII/II processes and an intervalence charge transfer (IVCT) transition in the one‐electron oxidized state. The potential separation (ΔE) of 12+–102+ has been correlated to the energy difference ΔG0, the energy of the IVCT band Eop, and the ground‐state delocalization coefficient α2. Time‐dependent (TD)DFT calculations suggest that the absorptions in the visible region of 12+–62+ are mainly associated with the metal‐to‐ligand charge‐transfer transitions from both ruthenium ions and to both terminal ligands and the bridging ligand. However, the energies of these transitions vary significantly. DFT calculations have been performed on 12+–62+ and 13+–63+ to give information on the electronic structures and spin populations of the mixed‐valent compounds. The TDDFT‐predicted IVCT excitations reproduce well the experimental trends in transition energies. In addition, three monoruthenium complexes have been synthesized for a comparison study.
Small Molecules that Target the Toxic RNA in Myotonic Dystrophy Type 2
Authors: Nguyen Lien , Lee JuYeon , Wong Chun‐Ho , Zimmerman Steven C. 
Published: June 2014

AbstractMyotonic dystrophy type 2 (DM2) is caused by an expansion of CCTG repeats in the zinc‐finger protein gene (ZNF9). Transcribed CCUG repeats sequester muscleblind‐like protein 1 (MBNL1), an important alternative splicing regulator, preventing its normal function, leading to the disease phenotype. We describe a series of ligands that disrupt the MBNL1–r(CCUG)n interaction as potential lead agents for developing DM2 therapeutics. A previously reported triaminopyrimidine–acridine conjugate was a moderate inhibitor in vitro, however it proved to be poorly water‐soluble and not cell‐permeable. To improve its therapeutic potential, the new set of ligands maintained the key triaminopyrimidine recognition unit but replaced the acridine intercalator with a bisamidinium groove binder. The optimized ligands exhibit low micromolar inhibition potency to MBNL1–r(CCUG)8. Importantly, the ligands are the first to show the ability to disrupt the MBNL1–r(CCUG)n foci in DM2 model cell culture and exhibit low cytotoxicity.
Childhood anxiety trajectories and adolescent disordered eating: Findings from the NICHD study of early child care and youth development
Authors: Zerwas Stephanie , Holle Ann Von , Watson Hunna , Gottfredson Nisha , Bulik Cynthia M. 
Published: June 2014

ABSTRACTObjectiveThe goal of the present article was to examine whether childhood anxiety trajectories predict eating psychopathology. We predicted that girls with trajectories of increasing anxiety across childhood would have significantly greater risk of disordered eating in adolescence in comparison to girls with stable or decreasing trajectories of anxiety over childhood.MethodData were collected as part of the prospective longitudinal NICHD Study of Early Child Care and Youth Development (N = 450 girls). Childhood anxiety was assessed yearly (54 months through 6th grade) via maternal report on the Child Behavior Checklist. Disordered eating behaviors were assessed at age 15 via adolescent self‐report on the Eating Attitudes Test (EAT‐26). We conducted latent growth mixture modeling to define girls' childhood anxiety trajectories. Maternal sensitivity, maternal postpartum depression, maternal anxiety, and child temperament were included as predictors of trajectory membership.ResultsThe best fitting model included three trajectories of childhood anxiety, the low‐decreasing class (22.9% of girls), the high‐increasing class (35.4%), and the high‐decreasing class (41.6%). Mothers with more symptoms of depression and separation anxiety had girls who were significantly more likely to belong to the high‐increasing anxiety trajectory. There were no significant differences in adolescent disordered eating for girls across the three childhood anxiety trajectories.DiscussionChildhood anxiety, as captured by maternal report, may not be the most robust predictor of adolescent disordered eating and may be of limited utility for prevention programs that aim to identify children in the community at greatest risk for disordered eating. © 2014 Wiley Periodicals, Inc. (Int J Eat Disord 2014; 47:784–792)
Effects of obstetric complications on volume and functional connectivity of striatum in anorexia nervosa patients
Authors: Favaro Angela , Tenconi Elena , Degortes Daniela , Manara Renzo , Santonastaso Paolo 
Published: June 2014

ABSTRACTObjectiveTo investigate the volume and functional connectivity of dorsal and ventral striatal nuclei in anorexia nervosa (AN) and their relationship with early exposure to obstetric complications.MethodFifty‐one patients with lifetime AN (35 acute, 16 recovered) and 34 healthy controls underwent high‐resolution and resting‐state functional magnetic resonance imaging.ResultsThe AN group showed reduced functional connectivity of the putamen compared with healthy women, and this reduction was more evident in patients with lifetime binge eating/purging. Both acute and recovered AN groups showed a larger left accumbens area compared with that of healthy women. The functional connectivity of bilateral nucleus accumbens and putamen showed significant negative correlations with number of obstetric complications in the AN group.DiscussionThis study supports the hypothesis that AN is associated with structural and functional alterations of striatal networks, and reveals the possible role of obstetric complications in the pathogenesis of striatal dysfunction. © 2014 Wiley Periodicals, Inc. (Int J Eat Disord 2014; 47:686–695)
The Impact of Anion‐Modulated Structural Variations on the Magnetic Coupling in Trinuclear Heterometallic CuII–CoII Complexes Derived from a Salen‐Type Schiff Base Ligand
Authors: Ghosh Soumavo , Aromí Guillem , Gamez Patrick , Ghosh Ashutosh 
Published: June 2014

AbstractThree new trinuclear heterometallic [(CuIIL)2CoIIX2] complexes [H2L = N,N′‐bis(salicylidene)‐1,3‐propanediamine and X = thiocyanate (1), benzoate (2), or azide (3)] have been synthesized by reacting the metalloligand [CuL] with Co(ClO4)2·6H2O and the NH4+ or Na+ salt of the corresponding anion in methanol. Structural characterization reveals that the central CoII ion is connected to two terminal metalloligands through μ1,1‐diphenoxido bridges in all three complexes. However, two monodentate thiocyanato ions, which are mutually cis coordinated to the Co atom in 1, generate a “bent” structure, whereas the trans‐coordinated syn–syn bridging benzoato (1κO:2κO′) and the end‐on bridging azido (μ1,1) coligands in 2 and 3, respectively, produce linear structures. The changes in the number and nature of the bridges with a shortening of the distances between the metal centers leads to a concomitant decrease of the average CuII–O–CoII bridging angle from 99.3(2) to 97.1(4) and 91.5(1)° for 1, 2 and 3, respectively. Variable‐temperature magnetic susceptibility measurements show the presence of a dominant antiferromagnetic coupling between the Cu–Co pairs in all three complexes. However, a steady decrease of the magnitude of the exchange coupling constant (JCu‐Co) is observed from –33.4 (for 1) to –11.4 (for 2) and –2.15 cm–1 (for 3). This trend suggests that larger Cu–O–Co angles are associated with stronger antiferromagnetic coupling.
Compactly Fused o‐Quinone‐Extended Tetrathiafulvalene‐o‐Quinone Triad – a Redox‐Amphoteric Ligand
Authors: Chalkov Nikolay O. , Cherkasov Vladimir K. , Abakumov Gleb A. , Romanenko Galina V. , Ketkov Sergey Yu. , Smolyaninov Ivan V. , Starikov Andrey G. , Kuropatov Viacheslav A. 
Published: June 2014

AbstractA new redox‐amphoteric ligand comprising a p‐phenylene‐extended tetrathiafulvalene (TTF) core and two o‐quinone termini has been synthesized. This work was performed in an attempt to synthesize a bridging ligand by combining one of the most powerful organic donors with strong acceptor units in a single molecule. The product was isolated in the doubly reduced diprotonated form. An X‐ray diffraction study revealed a rigid and planar structure for this molecule. This is the first example of an air‐stable p‐phenylene‐extended TTF with an unprotected central ring. The diquinone form itself has been prepared by oxidation of the doubly reduced diprotonated species and then characterized in solution. The electronic spectrum of this compound contains an intense peak that corresponds to intramolecular charge transfer. The spectroscopic and structural studies of both compounds were accompanied by DFT calculations. A singlet biradical ground state was predicted for the doubly reduced diprotonated form.
Total Synthesis and Configurational Validation of (+)‐Violapyrone C
Authors: Lee Jong Seok , Shin Junho , Shin Hee Jae , Lee Hwa‐Sun , Lee Yeon‐Ju , Lee Hyi‐Seung , Won Hoshik 
Published: June 2014

AbstractGold(I)‐catalyzed intramolecular 6‐endo‐dig cyclization of tert‐butyl ynoates afforded α‐pyrone cores of violapyrones. Moreover, this reaction was successfully applied to the stereospecific syntheses of (+)‐ and (–)‐violapyrone C, which allowed the absolute configuration of natural (+)‐violapyrone C to be assigned by comparison of the optical rotations. This first total synthesis, which proceeded in 22 % yield over 10 steps from (S)‐(–)‐2‐methylbutanol, features silver(I) oxide promoted monobenzylation of 1,4‐butanediol, Wittig olefination, Claisen condensation, Corey–Fuchs reaction, and gold(I)‐catalyzed α‐pyrone synthesis.