bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerated 1H MRSI using randomly undersampled spiral‐based k‐space trajectories
Authors: Chatnuntawech Itthi , Gagoski Borjan , Bilgic Berkin , Cauley Stephen F. , Setsompop Kawin , Adalsteinsson Elfar 
Published: July 2014

PurposeTo develop and evaluate the performance of an acquisition and reconstruction method for accelerated MR spectroscopic imaging (MRSI) through undersampling of spiral trajectories.Theory and MethodsA randomly undersampled spiral acquisition and sensitivity encoding (SENSE) with total variation (TV) regularization, random SENSE+TV, is developed and evaluated on single‐slice numerical phantom, in vivo single‐slice MRSI, and in vivo three‐dimensional (3D)‐MRSI at 3 Tesla. Random SENSE+TV was compared with five alternative methods for accelerated MRSI.ResultsFor the in vivo single‐slice MRSI, random SENSE+TV yields up to 2.7 and 2 times reduction in root‐mean‐square error (RMSE) of reconstructed N‐acetyl aspartate (NAA), creatine, and choline maps, compared with the denoised fully sampled and uniformly undersampled SENSE+TV methods with the same acquisition time, respectively. For the in vivo 3D‐MRSI, random SENSE+TV yields up to 1.6 times reduction in RMSE, compared with uniform SENSE+TV. Furthermore, by using random SENSE+TV, we have demonstrated on the in vivo single‐slice and 3D‐MRSI that acceleration factors of 4.5 and 4 are achievable with the same quality as the fully sampled data, as measured by RMSE of reconstructed NAA map, respectively.ConclusionWith the same scan time, random SENSE+TV yields lower RMSEs of metabolite maps than other methods evaluated. Random SENSE+TV achieves up to 4.5‐fold acceleration with comparable data quality as the fully sampled acquisition. Magn Reson Med 74:13–24, 2015. © 2014 Wiley Periodicals, Inc.
PAK1 mediates pancreatic cancer cell migration and resistance to MET inhibition
Authors: Zhou Wei , Jubb Adrian M , Lyle Karen , Xiao Qian , Ong Christy C , Desai Rupal , Fu Ling , Gnad Florian , Song Qinghua , Haverty Peter M , Aust Daniela , Grützmann Robert , Romero Mally , Totpal Klara , Neve Richard M , Yan Yibing , Forrest William F , Wang Yulei , Raja Rajiv , Pilarsky Christian , de Jesus‐Acosta Ana , Belvin Marcia , Friedman Lori S , Merchant Mark , Jaffee Elizabeth M , Zheng Lei , Koeppen Hartmut , Hoeflich Klaus P 
Published: July 2014

AbstractPancreatic adenocarcinoma (PDAC) is a major unmet medical need and a deeper understanding of molecular drivers is needed to advance therapeutic options for patients. We report here that p21‐activated kinase 1 (PAK1) is a central node in PDAC cells downstream of multiple growth factor signalling pathways, including hepatocyte growth factor (HGF) and MET receptor tyrosine kinase. PAK1 inhibition blocks signalling to cytoskeletal effectors and tumour cell motility driven by HGF/MET. MET antagonists, such as onartuzumab and crizotinib, are currently in clinical development. Given that even highly effective therapies have resistance mechanisms, we show that combination with PAK1 inhibition overcomes potential resistance mechanisms mediated either by activation of parallel growth factor pathways or by direct amplification of PAK1. Inhibition of PAK1 attenuated in vivo tumour growth and metastasis in a model of pancreatic adenocarcinoma. In human tissues, PAK1 is highly expressed in a proportion of PDACs (33% IHC score 2 or 3; n = 304) and its expression is significantly associated with MET positivity (p < 0.0001) and linked to a widespread metastatic pattern in patients (p = 0.067). Taken together, our results provide evidence for a functional role of MET/PAK1 signalling in pancreatic adenocarcinoma and support further characterization of therapeutic inhibitors in this indication. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd
Detonation Failure Characterization of Homemade Explosives
Authors: Janesheski Robert S. , Groven Lori J. , Son Steven F. 
Published: July 2014

AbstractTypically characterizing home made explosives (HMEs) requires many large scale experiments, which is prohibitive given the large number of materials in use. A small scale experiment was developed to characterize HMEs such as ammonium nitrate‐fuel oil mixtures. A microwave interferometer is applied to small scale confined transient experiments, yielding time resolved characterization of a failing detonation that is initiated with an ideal explosive booster charge. Experiments were performed with ammonium nitrate and two fuel compositions (diesel fuel and mineral oil). It was observed that the failure dynamics were influenced by factors such as the chemical composition, confiner thickness, and applied shock wave strength. Thin steel walled confiners with 0.71 mm wall thickness experienced detonation failure and decoupling of the shock wave from the reaction zone. Confiners with a wall thickness of 34.9 mm showed a decrease in propagation speed and a steady reactive wave was achieved. Varying the applied shock strength by using an attenuator showed corresponding changes in the initial overdriven reactive wave velocity in the HMEs. The distance to detonation failure was also shown to depend on the attenuator length when thin wall confinement was used. This experimental method is shown to be repeatable and can be performed with little required material (about 2 g). The data obtained could be useful to model development and validation, as well as quantifying detonability of materials.
STRengthening Analytical Thinking for Observational Studies: the STRATOS initiative
Authors: Sauerbrei Willi , Abrahamowicz Michal , Altman Douglas G. , le Cessie Saskia , Carpenter James ,   on behalf of the STRATOS initiative
Published: July 2014

The validity and practical utility of observational medical research depends critically on good study design, excellent data quality, appropriate statistical methods and accurate interpretation of results. Statistical methodology has seen substantial development in recent times. Unfortunately, many of these methodological developments are ignored in practice. Consequently, design and analysis of observational studies often exhibit serious weaknesses. The lack of guidance on vital practical issues discourages many applied researchers from using more sophisticated and possibly more appropriate methods when analyzing observational studies. Furthermore, many analyses are conducted by researchers with a relatively weak statistical background and limited experience in using statistical methodology and software. Consequently, even ‘standard’ analyses reported in the medical literature are often flawed, casting doubt on their results and conclusions. An efficient way to help researchers to keep up with recent methodological developments is to develop guidance documents that are spread to the research community at large.These observations led to the initiation of the strengthening analytical thinking for observational studies (STRATOS) initiative, a large collaboration of experts in many different areas of biostatistical research. The objective of STRATOS is to provide accessible and accurate guidance in the design and analysis of observational studies. The guidance is intended for applied statisticians and other data analysts with varying levels of statistical education, experience and interests.In this article, we introduce the STRATOS initiative and its main aims, present the need for guidance documents and outline the planned approach and progress so far. We encourage other biostatisticians to become involved. © 2014 The Authors.Statistics in Medicinepublished by John Wiley & Sons, Ltd.
Concise Review: Genomic Instability in Human Stem Cells: Current Status and Future Challenges
Authors: Oliveira Pedro H. , Silva Cláudia Lobato , Cabral Joaquim M.S. 
Published: July 2014

Abstract
Genomic instability is recognized as one of the most important hurdles in the expanding field of stem cell-based therapies. In the recent years, an accumulating body of evidence has shown that human stem cells undergo a diverse program of biological changes upon ex vivo cultivation that include numerical and structural chromosomal abnormalities, point mutations, variation of telomere length, and epigenetic instability. As the field moves forward, the growing awareness of the risk factors associated with human genome plasticity strongly advocates for the use of extensive genetic screening as part of a quality control platform to attest to the safety of stem cell-based products. Here we present a timely and comprehensive review that addresses the current status and emerging trends of the field, ultimately underscoring the need to implement new regulatory standards able to streamline the route to therapeutic applications. Stem Cells 2014;32:2824–2832
Concise Reviews: Cancer Stem Cells: From Concept to Cure
Authors: Matchett K. B. , Lappin T. R. 
Published: July 2014

Abstract
In 1953, noting a remarkable consistency between the agents causing mutations and those associated with cancer, Carl Nordling, a Finnish-born architect, proposed that cancer results from an accumulation of genetic mutations. It is now generally accepted that inherited mutations and environmental carcinogens can lead to the development of premalignant clones. After further mutations, one cell reaches a critical state which confers a survival or growth advantage over normal cells. Such cells have the ability to initiate a malignant tumour. They share many of the features of normal stem cells, including the capacity for self-renewal and differentiation, and are widely termed cancer stem cells (CSCs). Although CSCs have been well characterized in hematological malignancies, their existence in some other tissues has been questioned. Here, we review recent work in which stem cells and stem cell-like cells have been used to investigate the pathogenesis of cancer and potential anticancer treatment strategies, in the context of both hematological and somatic tissue disease. Stem Cells 2014;32:2563–2570
Predicting enzymatic reactivity: from theory to design
Authors: Świderek Katarzyna , Tuñón Iñaki , Moliner Vicent 
Published: July 2014

Theoretical and computational tools can provide a detailed knowledge of the mode of action of enzymes. This knowledge can be systematized to be used as a guide for the design of new biocatalysts for industrial purposes. In this article, we illustrate the current view about the origin of enzymatic catalysis based on molecular simulations and its use in the design of new enzymes. Transition‐state stabilization in a preorganized active site seems to be the major source of catalysis, although some degree of protein flexibility is needed to reach the maximum catalytic efficiency. Development of a new enzyme must then consider the inclusion of TS stabilizing interactions either in a preexisting enzymatic structure (enzymatic redesign) or in a completely new designed enzyme (de novo design). However, the lack of a detailed understanding of the link between sequence, structure, flexibility, and function still prevents the complete success of these strategies. WIREs Comput Mol Sci 2014, 4:407–421.This article is categorized under:

Structure and Mechanism > Computational Biochemistry and Biophysics
Electronic Structure Theory > Combined QM/MM Methods
Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Novel Dinuclear Redox‐isomeric Complexes with a Tetrapodal Pyridine‐based Ligand
Authors: Bubnov Michael P. , Skorodumova Nina A. , Zolotukhin Alexey A. , Arapova Alla V. , Baranov Evgenii V. , Stritt Anika , Ünal Alper , Grohmann Andreas , Heinemann Frank W. , Bogomyakov Artem S. , Smirnova Natal'a N. , Cherkasov Vladimir K. , Abakumov Gleb A. 
Published: July 2014

AbstractTris‐o‐semiquinonato cobalt complexes react with a tetrapodal pyridine‐derived ligand to form dinuclear cobalt compounds of general formula (OMP)[CoQ2]2, where OMP = 2,2′‐(pyridine‐2,6‐diyl)bis(N1,N1,N3,N3‐tetramethylpropane‐1,3‐diamine), Q = mono‐ or dianion of 3,6‐di‐tert‐butyl‐o‐benzoquinone (complex 1) and it derivatives: 3,6‐di‐tert‐butyl‐4,5‐N,N′‐piperazino‐o‐benzoquinone (complex 2), and 3,6‐di‐tert‐butyl‐4‐Cl‐o‐benzoquinone (complex 3). Single crystal X‐ray crystallography of 1 and 3 indicates two bis‐quinonato cobalt units bound by an OMP ligand, which acts as a bridge. Each central cobalt atom is chelated by one N1,N1,N3,N3‐tetramethylpropane‐1,3‐diamine and two o‐quinonato fragments. The nitrogen atom of the pyridine ring is uncoordinated. All complexes were characterized by NIR‐IR and EPR spectroscopy, precise adiabatic vacuum calorimetry, and by variable‐temperature magnetic susceptibility measurements. All data indicate a reversible thermally driven redox‐isomeric (valence tautomeric) transformation in the solid state for all complexes.
On The Steric Hindrance of Bulky Substituents – Determination of Their Cone Angles
Authors: Schulz Axel 
Published: July 2014

AbstractA series of simple halogen compounds was studied with respect to steric hindrance by means of quantum mechanical methods utilizing the M062X/aug‐cc‐pvdz level of theory. The maximal cone angles of the halogen compounds R–E were computed for a series of different substituents (R carbon or silyl based substituents, E = halogen). Depending on the substitution pattern and the bulkiness of the substituent R a correlation between the cone angle and structural parameters is discussed. Estimates for the cone angles of any element attached to R are provided, that allows comparison of cone angles of different substituents at different distances, which can facilitate synthesis. Additionally, the bonding situation was assessed by natural bond orbital (NBO) analysis indicating that significant electronic effects should be considered when changing from silyl to carbon based substituents. Silyl based substituents display a considerably larger charge transfer to E compared to carbon based once.
The development of perceived maternal hostile, aggressive conflict from adolescence to early adulthood: Antecedents and outcomes
Authors: Castellani Valeria , Pastorelli Concetta , Eisenberg Nancy , Caffo Ernesto , Forresi Barbara , Gerbino Maria 
Published: July 2014

ABSTRACTThe goal of this study was to investigate the development of mother–adolescent hostile aggressive conflict (MHAC) from late adolescence to young adulthood. The role of child’ depressive and delinquency problems and family characteristics, as well as the relation of level and change in MHAC to adolescents' delinquency and depression in early adulthood will be investigated. From the Genzano Longitudinal study 385 adolescents (51% males) participated in this study and completed self report measures. Latent growth curve modeling, separately by gender, indicated that the overall level MHAC exhibited a modest decline over time. For both males and females, depressive problems were associated to higher initial levels of MHAC and early maternal age predicted less decline of MHAC. Starting levels of MHAC were associated with Delinquency in males and with Depression in females, while the growth of MHAC was associated to delinquency in males and females and to depression in males.
The role of a neuropsychiatry clinic in a tertiary referral teaching hospital: a 2-year study
Authors: Jabbar F. , Doherty A. , Duffy R. , Aziz M. , Casey P. , Sheehan J. , Lynch T. , Kelly B. D. 
Published: July 2014

ObjectivesMental disorder is common among individuals with neurological illness. We aimed to characterise the patient population referred for psychiatry assessment at a tertiary neurology service in terms of neurological and psychiatric diagnoses and interventions provided.MethodsWe studied all individuals referred for psychiatry assessment at a tertiary neurology service over a 2-year period (n= 82).ResultsThe most common neurological diagnoses among those referred were epilepsy (16%), Parkinson’s disease (15%) and multiple sclerosis (8%). The most common reasons for psychiatric assessment were low mood or anxiety (48%) and medically unexplained symptoms or apparent functional or psychogenic disease (21%). The most common diagnoses among those with mental disorder were mood disorders (62%), and neurotic, stress-related and somatoform disorders, including dissociative (conversion) disorders (28%). Psychiatric diagnosis was not related to gender, neurological diagnosis or psychiatric history.ConclusionIndividuals with neurological illness demonstrate significant symptoms of a range of mental disorders. There is a need for further research into the characteristics and distribution of mental disorder in individuals with neurological illness, and for the enhancement of integrated psychiatric and neurological services to address the comorbidities demonstrated in this population.
Deformation statistics of sub-Kolmogorov-scale ellipsoidal neutrally buoyant drops in isotropic turbulence
Authors: Biferale L. , Meneveau C. , Verzicco R. 
Published: July 2014

AbstractSmall droplets in turbulent flows can undergo highly variable deformations and orientational dynamics. For neutrally buoyant droplets smaller than the Kolmogorov scale, the dominant effects from the surrounding turbulent flow arise through Lagrangian time histories of the velocity gradient tensor. Here we study the evolution of representative droplets using a model that includes rotation and stretching effects from the surrounding fluid, and restoration effects from surface tension including a constant droplet volume constraint, while assuming that the droplets maintain an ellipsoidal shape. The model is combined with Lagrangian time histories of the velocity gradient tensor extracted from direct numerical simulations (DNS) of turbulence to obtain simulated droplet evolutions. These are used to characterize the size, shape and orientation statistics of small droplets in turbulence. A critical capillary number is identified associated with unbounded growth of one or two of the droplet’s semi-axes. Exploiting analogies with dynamics of polymers in turbulence, the critical capillary number can be predicted based on the large deviation theory for the largest finite-time Lyapunov exponent quantifying the chaotic separation of particle trajectories. Also, for subcritical capillary numbers near the critical value, the theory enables predictions of the slope of the power-law tails of droplet size distributions in turbulence. For cases when the viscosities of droplet and outer fluid differ in a way that enables vorticity to decorrelate the shape from the straining directions, the large deviation formalism based on the stretching properties of the velocity gradient tensor loses validity and its predictions fail. Even considering the limitations of the assumed ellipsoidal droplet shape, the results highlight the complex coupling between droplet deformation, orientation and the local fluid velocity gradient tensor to be expected when small viscous drops interact with turbulent flows. The results also underscore the usefulness of large deviation theory to model these highly complex couplings and fluctuations in turbulence that result from time integrated effects of fluid deformations.
Turbulent Schmidt number and eddy diffusivity change with a chemical reaction
Authors: Watanabe Tomoaki , Sakai Yasuhiko , Nagata Kouji , Terashima Osamu 
Published: July 2014

AbstractWe provide empirical evidence that the eddy diffusivity$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}D_{{t}\alpha }$and the turbulent Schmidt number${\mathit{Sc}}_{{t}\alpha }$of species$\alpha $($\alpha =\mathrm{A}, \mathrm{B}$or$\mathrm{R}$) change with a second-order chemical reaction ($\mathrm{A} + \mathrm{B} \rightarrow \mathrm{R}$). In this study, concentrations of the reactive species and axial velocity are simultaneously measured in a planar liquid jet. Reactant A is premixed into the jet flow and reactant B is premixed into the ambient flow. An optical fibre probe based on light absorption spectrometry is combined with I-type hot-film anemometry to simultaneously measure concentration and velocity in the reactive flow. The eddy diffusivities and the turbulent Schmidt numbers are estimated from the simultaneous measurement results. The results show that the chemical reaction increases${\mathit{Sc}}_{t\mathrm{A}}$;${\mathit{Sc}}_{t\mathrm{B}}$is negative in the region where the mean concentration of reactant B decreases in the downstream direction, and is positive in the non-reactive flow in the entire region on the jet centreline. It is also shown that${\mathit{Sc}}_{t\mathrm{R}}$is positive in the upstream region whereas it is negative in the downstream region. The production terms of axial turbulent mass fluxes of reactant B and product R can produce axial turbulent mass fluxes opposite to the axial gradients of the mean concentrations. The changes in the production terms due to the chemical reaction result in the negative turbulent Schmidt number of these species. These results imply that the gradient diffusion model using a global constant turbulent Schmidt number poorly predicts turbulent mass fluxes in reactive flows.
Highly resolved pulsatile flows through prosthetic heart valves using the entropic lattice-Boltzmann method
Authors: Yun B. Min , Dasi L. P. , Aidun C. K. , Yoganathan A. P. 
Published: July 2014

AbstractProsthetic heart valves have been widely used to replace diseased or defective native heart valves. Flow through bileaflet mechanical heart valves (BMHVs) have previously demonstrated complex phenomena in the vicinity of the valve owing to the presence of two rigid leaflets. This study aims to accurately capture the complex flow dynamics for pulsatile flow through a 23 mm St Jude Medical (SJM) Regent™ BMHV. The lattice-Boltzmann method (LBM) is used to simulate pulsatile flow through the valve with the inclusion of reverse leakage flow at very high spatiotemporal resolution that can capture fine details in the pulsatile BMHV flow field. For higher-Reynolds-number flows, this high spatiotemporal resolution captures features that have not been observed in previous coarse resolution studies. In addition, the simulations are able to capture with detail the features of leaflet closing and the asymmetric b-datum leakage jet during mid-diastole. Novel flow physics are visualized and discussed along with quantification of turbulent features of this flow, which is made possible by this parallelized numerical method.