bluuebunny/crossref_metadata_2025 huggingface dataset:
Action minimization and macroscopic interface motion under forced displacement
Authors: Birmpa Panagiota , Tsagkarogiannis Dimitrios
Published: March 2017

We study an one dimensional model where an interface is the stationary solution of a mesoscopic non local evolution equation which has been derived by a microscopic stochastic spin system. Deviations from this evolution equation can be quantified by obtaining the large deviations cost functional from the underlying stochastic process. For such a functional, derived in a companion paper, we investigate the optimal way for a macroscopic interface to move from an initial to a final position distant by R within fixed time T. We find that for small values of R∕T the interface moves with a constant speed, while for larger values there appear nucleations of the other phase ahead of the front.
RAI1 Overexpression Promotes Altered Circadian Gene Expression and Dyssomnia in Potocki–Lupski Syndrome
Authors: Mullegama Sureni , Alaimo Joseph , Fountain Michael , Burns Brooke , Balog Amanda , Chen Li , Elsea Sarah
Published: March 2017

Retinoic acid induced 1 (RAI1) encodes a dosage-sensitive gene that when haploinsufficient results in Smith–Magenis syndrome (SMS) and when overexpressed results in Potocki–Lupski syndrome (PTLS). Phenotypic and molecular evidence illustrates that haploinsufficiency of RAI1 disrupts circadian rhythm through the dysregulation of the master circadian regulator, circadian locomotor output cycles kaput (CLOCK), and other core circadian components, contributing to prominent sleep disturbances in SMS. However, the phenotypic and molecular characterization of sleep features in PTLS has not been elucidated. Using the Pittsburgh Sleep Quality Index (PSQI), caregivers of 15 school-aged children with PTLS reported difficulties in initiating sleep. Indeed, more than 70% of individuals manifested moderate to severe sleep latency, as defined by the PSQI. Moreover, these individuals manifested difficulties in sleep maintenance, with middle of the night and early morning awakenings. When assessing daytime sleepiness through the Epworth Sleepiness Scale, approximately 21% of the individuals manifested excessive daytime somnolence. This indicates that mild dyssomnia characterizes the majority of the sleep phenotype, with occasionally problematic daytime somnolence, a phenotype different than that expressed by individuals with SMS, where daytime sleepiness is a chronic problem. Gene expression analysis of the core circadian machinery in the hypothalamus of the PTLS mouse model (Rai1-Tg) found significant dysregulation of the transcriptional activators, Clock and Arntl, and the transcriptional repressors, Per1–3 and Cry1/2, during both light and dark phases. These findings suggest a partial loss of circadian entrainment typically evoked by environmental photic cues. Examination of circadian clock gene expression in the Rai1-Tg mouse heart, liver, and kidney found unchanged expression of Clock and most of its downstream targets during both light and dark phases, suggesting an asynchronized circadian rhythm. Furthermore, examination of circadian gene expression in synchronized PTLS lymphoblasts revealed reduced transcripts of the Period (PER1–3) family and normal expression of CRY1/2. The finding that central circadian gene expression was altered while many peripheral circadian components were intact suggests a tissue-specific circadian uncoupling of the circadian machinery due to Rai1 overexpression. Overall, our results demonstrate that overexpression of RAI1 results in sleep deficiencies in individuals with PTLS due to a lack of properly regulated circadian machinery gene expression and highlight the importance of evaluating sleep concerns in individuals with PTLS.
Hollow Fiber Oxygenator Composition Has a Significant Impact on Failure Rates in Neonates on Extracorporeal Membrane Oxygenation: A Retrospective Analysis
Authors: Bernard Philip , Skinner Sean , Bhandary Prasad , Ruzic Ana , Bacon Matthew , Ballard Hubert , Daniel John
Published: March 2017

In extracorporeal life support (ECLS), there are two main types of oxygenators in clinical use for neonates: polymethylpentene (PMP) hollow fiber and polypropylene (PP) hollow fiber. A retrospective study was performed on neonates (n = 44) who had undergone ECLS for noncardiac indications from 2009 to 2015. Between the two groups (PMP n = 21, PP n = 23), the PP oxygenators failed 91% of the time, whereas the PMP oxygenators failed 43% of the time (p < 0.05). Analysis suggests PMP oxygenators are less prone to failure than PP oxygenators, and they require fewer number of oxygenator changes during a neonatal ECLS.
Unusual de novo Partial Trisomy 17p12p11.2 due to Unbalanced Insertion into 5p13.1 in a Severely Affected Boy
Authors: Mendez-Rosado Luis , Lantigua Araceli , Galarza Juan , Hamid Al-Rikabi Ahmed , Ziegler Monika , Liehr Thomas
Published: March 2017

Gain of copy numbers can be due to different chromosomal rearrangements such as direct or indirect duplications, translocations, small supernumerary marker chromosomes, or insertions. In a 3-year-old boy with dysmorphic features and developmental delay, chromosome analyses revealed a derivative chromosome 5. Microdissection and reverse fluorescence in situ hybridization identified the in 5p13.1 inserted part as 17p12-p11.2 material. Thus the patient suffered from a rare combination of genomic disorder, that is, Charcot-Marie-Tooth disease type 1A and Potocki-Lupski syndrome. Parental studies indicated that the abnormality was de novo in origin. As the question how this rearrangement arose cannot be answered conclusively, formal genetic counseling is warranted, which includes a discussion regarding the possibility of gonadal mosaicism. In conclusion, this case highlights that chromosome 17p is genetically relatively instable, and thus it can lead to rare chromosomal conditions.
Trajectory and chirality of vortex domain walls in ferromagnetic nanowires with an asymmetric Y-branch
Authors: Brandão J. , Mello A. , Garcia F. , Sampaio L. C.
Published: March 2017

The motion and trajectory of vortex domain walls (VDWs) driven by magnetic field were investigated in Fe80Ni20 nanowires with an asymmetric Y-shape branch. By using the focused magneto-optical Kerr effect, we have probed the injection, pinning, and propagation of VDWs in the branch and in the wire beyond the branch entrance. Hysteresis cycles measured at these points show 3 and 4 jumps in the magnetization reversal, respectively. Micromagnetic simulations were carried out to obtain the number of jumps in the hysteresis cycles, and the magnetization process involved in each jump. Based on simulations and from the size of the jumps in the measured hysteresis cycles, one obtains the histogram of the domain wall type probability. While in the branch domain walls of different types are equiprobable, in the nanowire vortex domain walls with counter clockwise and clockwise chiralities and transverse-down domain walls are measured with probabilities of 65%, 25%, and 10%, respectively. These results provide an additional route to select the trajectory and chirality of VDWs in magnetic nanostructures.
Unprecedented Al supersaturation in single-phase rock salt structure VAlN films by Al+ subplantation
Authors: Greczynski G. , Mráz S. , Hans M. , Primetzhofer D. , Lu J. , Hultman L. , Schneider J. M.
Published: March 2017

Modern applications of refractory ceramic thin films, predominantly as wear-protective coatings on cutting tools and on components utilized in automotive engines, require a combination of excellent mechanical properties, thermal stability, and oxidation resistance. Conventional design approaches for transition metal nitride coatings with improved thermal and chemical stability are based on alloying with Al. It is well known that the solubility of Al in NaCl-structure transition metal nitrides is limited. Hence, the great challenge is to increase the Al concentration substantially while avoiding precipitation of the thermodynamically favored wurtzite-AlN phase, which is detrimental to mechanical properties. Here, we use VAlN as a model system to illustrate a new concept for the synthesis of metastable single-phase NaCl-structure thin films with the Al content far beyond solubility limits obtained with conventional plasma processes. This supersaturation is achieved by separating the film-forming species in time and energy domains through synchronization of the 70-μs-long pulsed substrate bias with intense periodic fluxes of energetic Al+ metal ions during reactive hybrid high power impulse magnetron sputtering of the Al target and direct current magnetron sputtering of the V target in the Ar/N2 gas mixture. Hereby, Al is subplanted into the cubic VN grains formed by the continuous flux of low-energy V neutrals. We show that Al subplantation enables an unprecedented 42% increase in metastable Al solubility limit in V1-xAlxN, from x = 0.52 obtained with the conventional method to 0.75. The elastic modulus is 325 ± 5 GPa, in excellent agreement with density functional theory calculations, and approximately 50% higher than for corresponding films grown by dc magnetron sputtering. The extension of the presented strategy to other Al-ion-assisted vapor deposition methods or materials systems is straightforward, which opens up the way for producing supersaturated single-phase functional ceramic alloy thin films combining excellent mechanical properties with high oxidation resistance.
Ab initio research of energy loss for energetic protons in solid-density Be
Authors: He Bin , Meng Xu-Jun , Wang Zhi-Gang , Wang Jian-Guo
Published: March 2017

Ab initio research of energy loss for energetic protons in solid-density Be is made based on the average atom model. Our results are found in good agreement with the recent experiment for both warm and cool matter. Our results are compared with the local density approximation model and the reason for their difference is also explored. The energy loss at smaller projectile energies is predicted by our model and local density approximation, which helps probe the higher reliability of the proving model and judge the existence of the non-Fermi-Dirac velocity distribution for free electrons exists in dense plasmas in future.
Zinc blende-oxide phase transformation upon oxygen annealing of ZnSe shell in ZnO-ZnSe core-shell nanowires
Authors: Jabri S. , Amiri G. , Hassani S. , Lusson A. , Sallet V. , Meftah A. , Galtier P. , Oueslati M.
Published: March 2017

ZnO-ZnSe core-shell nanowires have been grown by metal organic chemical vapor deposition and subsequently annealed in an O2 atmosphere. It has been found that the incorporation of oxygen into the ZnSe shell over the 470–580 °C temperature range results in a phase transformation from zinc Blende to orthorhombic and wurtzite. The X-ray diffraction pattern confirms that the heterostructures are composed of a wurtzite ZnO core and an oxide ZnSeO shell. The Raman spectroscopy study shows the appearance of additional peaks at 220 cm−1, 278 cm−1, 480 cm−1, 550 cm−1, and 568 cm−1, which reveal a phase transformation associated with the incorporation of the oxygen into the shell after annealing at 470 °C. This work opens a way to study the structure stability of ZnO-ZnSe core-shell nanowire production and help to understand the mechanisms of the oxidation in ZnO-ZnSe core-shell nanowires.
Impact of sputter-instigated plasmonic features in TCO films: for ultrathin photovoltaic applications
Authors: Awasthi Vishnu , Garg Vivek , Sengar Brajendra S. , Pandey Sushil Kumar , Aaryashree  , Kumar Shailendra , Mukherjee C. , Mukherjee Shaibal
Published: March 2017

The structural and optical properties of Ga-doped ZnO (GZO) and Ga-doped MgZnO (GMZO) individual films are analyzed. Sputter-instigated plasmonic features are observed in individual GZO and GMZO films due to the formation of metal and metal oxide nanoclusters. The plasmon generation is verified by electron energy loss spectra obtained by ultraviolet-photoelectron spectroscopy, spectroscopic ellipsometry, and field-emission scanning-electron microscopy measurements. This is promising in terms of increasing the efficiency of the solar cell by increasing the optical path length in the absorbing layer while keeping the same physical length by light scattering and trapping mechanism.
Dramatic variation of the multiferroic properties in Sr doped Ca1-xSrxMn7O12
Authors: Jain Parul , Saha J. , Gupta L. C. , Patnaik Satyabrata , Ganguli A. K. , Chatterjee Ratnamala
Published: March 2017

CaMn7O12 is a magnetic multiferroic material, in which large ferroelectric polarization has reportedly been induced by magnetic ordering. In this work, we observe remarkable changes in the spontaneous ferroelectric polarization PS as well as the magnetization M with only 2% Sr doping. In Ca0.98Sr0.02Mn7O12, PS dramatically becomes more than double the PS in the un-doped material and concomitantly M is reduced to less than half of its value therein. Increase of PS together with the decrease of M points out clearly the coupling of PS and M in CaMn7O12. We stress here that as Ca and Sr are isovalent, no charge carriers (electrons and holes) are added in the system due to Sr-doping. X-ray diffraction shows that all our Sr-doped materials Ca1-xSrxMn7O12 (x = 0.01, 0.02, 0.05, 0.10) are free from secondary phases. From our work, it becomes clear why SrMn7O12 exhibits no or weak ferroelectricity.
1-(+)-Dehydroabietylimidazolium Salts as Enantiomer Discriminators for NMR Spectroscopy
Authors: Gunaratne H. Q. Nimal , Laaksonen Tiina , Seddon Kenneth R. , Wähälä Kristiina
Published: March 2017

Nine new (+)-dehydroabietylimidazolium salts were synthesised and studied as chiral solvating agents for several different racemic aromatic and non-aromatic carboxylate salts. These cationic chiral solvating agents resolve racemic ionic analytes better than non-ionic ones. Bis(dehydroabietylimidazolium) bis(trifluoromethanesulfonimide) gave the best discrimination for the enantiomers of carboxylate salts. Its resolution behaviour was studied by an NMR titration experiment, which indicated 1 : 1 complexation with the racemic analyte. The dehydroabietylimidazolium salts were also useful in enantiomeric excess (ee) determinations, and for the recognition of chirality of racemic aromatic and non-aromatic α-substituted carboxylic acids.
Neural basis of impaired safety signaling in Obsessive Compulsive Disorder
Authors: Apergis-Schoute Annemieke M. , Gillan Claire M. , Fineberg Naomi A. , Fernandez-Egea Emilio , Sahakian Barbara J. , Robbins Trevor W.
Published: March 2017

Significance

Assigning safety to stimuli and situations forms an important part of everyday functioning. Obsessive Compulsive Disorder (OCD) is a prototypical disorder of inflexible behavior influenced by anxiety. Here we show, using neuroimaging of fear reversal learning, which involves a previously threatening stimulus becoming safe while a previously safe stimulus becomes threatening, that OCD patients fail to differentiate a safe from a threatening stimulus only after such a reversal, as measured by skin conductance responses. This OCD impairment in safety signaling, a likely prominent component of successful exposure therapy, is predicted and mediated by altered activity in a neural salience network including the ventromedial prefrontal cortex.
Higher-than-ballistic conduction of viscous electron flows
Authors: Guo Haoyu , Ilseven Ekin , Falkovich Gregory , Levitov Leonid S.
Published: March 2017

Significance

Free electron flows through constrictions in metals are often regarded as an ultimate high-conduction charge transfer. We predict that electron fluids can flow with a resistance that is much smaller than the fundamental quantum mechanical ballistic limit for nanoscale electronics. The “superballistic” low-dissipation transport is particularly striking for the flow through a viscous point contact, a constriction exhibiting the quantum mechanical ballistic transport at zero temperature but governed by viscous electron hydrodynamics at a higher temperature. Unlike other mechanisms of low-dissipation transport, for example, superconductivity, the viscous electron flows can be realized at elevated temperatures, granting a new route for the low-power electronics research.
Yellow taxis have fewer accidents than blue taxis because yellow is more visible than blue
Authors: Ho Teck-Hua , Chong Juin Kuan , Xia Xiaoyu
Published: March 2017

Significance

This paper examines the phenomenon that yellow taxis have fewer accidents than blue taxis. Statistical analysis of a unique and comprehensive dataset suggests that the higher visibility of the color yellow makes it easier for other drivers to avoid getting into accidents with yellow taxis, leading to a lower accident rate. This suggests that color visibility should play a major role in determining the colors used for public transport vehicles.
Amyotrophic lateral sclerosis-linked mutations increase the viscosity of liquid-like TDP-43 RNP granules in neurons
Authors: Gopal Pallavi P. , Nirschl Jeffrey J. , Klinman Eva , Holzbaur Erika L. F.
Published: March 2017

Significance

Mutations in TAR-DNA binding protein 43 (TDP-43), an RNA-binding protein (RBP) with multiple functions in RNA metabolism, cause amyotrophic lateral sclerosis (ALS), but it is uncertain how defects in RNA biology cause disease. Purified RNA-binding protein FUS and heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) form liquid droplets in vitro through liquid–liquid phase separation. However, the biophysical properties of ribonucleoprotein (RNP) granules composed of wild-type (WT) or ALS-linked TDP-43 have not been studied in primary neurons. We show that TDP-43 WT RNP granules exhibit distinct biophysical properties depending on their axonal location, whereas granules formed by ALS-linked mutant TDP-43 are more viscous and show disrupted axonal transport dynamics. We propose the distinct biophysical properties of these neuronal RNP granules may reflect different maturational states and differential propensity for pathological transformation.
Lys49 myotoxin from the Brazilian lancehead pit viper elicits pain through regulated ATP release
Authors: Zhang Chuchu , Medzihradszky Katalin F. , Sánchez Elda E. , Basbaum Allan I. , Julius David
Published: March 2017

Significance

Bites from venomous snakes can inflict substantial pain and inflammatory tissue damage. Snake phospholipase A2 (PLA2), and PLA2-like toxins that retain the PLA2 fold but lack enzymatic activity, are commonly found in snake venoms. In this study, we identify a PLA2-like toxin (BomoTx), from the Brazilian lancehead pit viper (
Bothrops moojeni
), that activates a subpopulation of somatosensory neurons that contribute to pain sensation. We show that BomoTx excites these neurons by stimulating the release of cellular ATP through a mechanism involving pannexin hemichannels. Consequent activation of purinergic receptors elicits acute pain, tissue inflammation, and pain hypersensitivity. Thus, we have elucidated the mechanism of action for a toxin from
Bothrops
snakes, which inflict a majority of bites in Latin America.
Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in
Pseudomonas aeruginosa
Authors: Racki Lisa R. , Tocheva Elitza I. , Dieterle Michael G. , Sullivan Meaghan C. , Jensen Grant J. , Newman Dianne K.
Published: March 2017

Significance

Quiescent bacteria are intrinsically resistant to antibiotics and the host immune response. A conserved bacterial starvation survival response is the consumption of ATP to make an inorganic polymer, polyphosphate (polyP), which then forms granule superstructures. PolyP granules occur in all three domains of life, yet how and why cells form these structures is poorly understood. Through high-resolution spatiotemporal characterization of de novo granule genesis, we find that polyP granule synthesis is required for and coordinated with cell cycle exit in the opportunistic pathogen
Pseudomonas aeruginosa
. PolyP has also been functionally connected with the cell cycle in eukaryotes, suggesting that polyP may be a broadly conserved mediator between metabolic state and the cell cycle.
Determining climate effects on US total agricultural productivity
Authors: Liang Xin-Zhong , Wu You , Chambers Robert G. , Schmoldt Daniel L. , Gao Wei , Liu Chaoshun , Liu Yan-An , Sun Chao , Kennedy Jennifer A.
Published: March 2017

Significance

Projections of the economic consequences of climate change are valuable for policy making but generally rely on integrated assessments that cannot account for highly localized climate effects. Most agricultural climate impact studies focus on local effects or partial productivity measures insufficient to capture national economic outcomes. Here, we directly link climate variables in specific US regions to total factor productivity (TFP). We quantify the national economic consequences of past climate variations, identify critical agricultural regions with national significance, and project future changes in TFP under different climate scenarios. We provide a physical understanding of these climate−economic links, show that the agricultural economy is becoming increasingly sensitive to climate, and lay a more concrete foundation for informed decision-making.
Spatial confinement of active microtubule networks induces large-scale rotational cytoplasmic flow
Authors: Suzuki Kazuya , Miyazaki Makito , Takagi Jun , Itabashi Takeshi , Ishiwata Shin’ichi
Published: March 2017

Significance

At the microscopic scale, collective behaviors of motile units can induce directed fluid flow on a larger length scale than individual units based on their hydrodynamic interactions. Here, we found that the motor-driven extensile behaviors of microtubule bundles in the cytoplasm induce rotational flow in a cell-sized confined space on length scale and timescale that were 10- to 100-fold longer than the vortex flows emerging in the bulk space. These scale differences were derived from mechanical force generation by microtubule bundle elongation near the physical boundary and the transmission of this force over the microtubule network. These findings suggest that the microtubule cytoskeleton utilizes not only hydrodynamic interactions but also mechanical interactions to induce large-scale cytoplasmic flow.
Electron transfer pathways in a multiheme cytochrome MtrF
Authors: Watanabe Hiroshi C. , Yamashita Yuki , Ishikita Hiroshi
Published: March 2017

Significance

Cellular respiration process in dissimilatory metal-reducing bacteria is coupled to electron transfer. In
Shewanella
species, a decaheme cytochrome MtrF transfers electrons to extracellular insoluble substrates, such as Fe(III) and Mn(III/IV). Using the atomic coordinates of the MtrF crystal structure and analyzing interactions with the protein environments, we calculated the redox potential (
E
m
) values of the 10 hemes in MtrF. The
E
m
profiles show how the electron transfer pathways proceed in MtrF. We showed that, when MtrF is reduced, the direction of the ET pathway switches, and bound flavin becomes the terminal electron acceptor.
Arsenic trioxide targets MTHFD1 and SUMO-dependent nuclear de novo thymidylate biosynthesis
Authors: Kamynina Elena , Lachenauer Erica R. , DiRisio Aislyn C. , Liebenthal Rebecca P. , Field Martha S. , Stover Patrick J.
Published: March 2017

Significance

We have identified de novo thymidylate biosynthesis as a target of arsenic at exposure levels observed in human populations. Arsenic enhances methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) small ubiquitin-like modifier (SUMO)-ylation and subsequent proteolytic degradation of MTHFD1 and serine hydroxymethyltransferase (SHMT), resulting in depressed rates of de novo thymidylate synthesis, elevated uracil levels in nuclear DNA, and increased genome instability. These findings provide a molecular mechanism linking clastogenic and teratogenic effects of arsenic to impaired de novo thymidylate synthesis.
Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor
Authors: Salvi Michele , Schomburg Benjamin , Giller Karin , Graf Sabrina , Unden Gottfried , Becker Stefan , Lange Adam , Griesinger Christian
Published: March 2017

Significance

Histidine kinases are key players in prokaryotic environment sensing. Citrate binding to the extracytoplasmic sensing domain of histidine kinase CitA triggers a contraction of the domain, resulting in a pull on the C-terminal β-strand. By a combination of liquid- and solid-state NMR spectroscopy, structural alterations observed for the isolated domain can be confirmed in context of its native environment as part of a membrane-embedded receptor. Our results demonstrate that the mechanistic model derived from the isolated ligand-sensing domain is compatible with the sensor in a native-like membrane environment and allows transfer of the model to transmembrane signaling by this class of sensor kinases.
The presumed ginkgophyteUmaltolepishas seed-bearing structures resembling those of Peltaspermales and Umkomasiales
Authors: Herrera Fabiany , Shi Gongle , Ichinnorov Niiden , Takahashi Masamichi , Bugdaeva Eugenia V. , Herendeen Patrick S. , Crane Peter R.
Published: March 2017

Significance

Understanding the origins of the five groups of living seed plants requires well-supported hypotheses of their relationships to extinct groups, many of which are poorly understood. New information from the Early Cretaceous of Mongolia on the enigmatic extinct plantUmaltolepisshows that its leaves are similar to those ofGinkgo, but its seed-bearing structures are unique, and more comparable to those of certain extinct Peltaspermales and Umkomasiales.Umaltolepisprovides new data for understanding relationships among living and fossil seed plants and supports previous ideas thatGinkgo bilobamay be the sole surviving relict of a once very diverse group of Mesozoic seed plants.
Effects of language impairment and bilingualism across domains
Authors: Blom Elma , Boerma Tessel
Published: March 2017

Purpose: This study examined the effects of language impairment (LI) and bilingualism across vocabulary, morphology and verbal memory in a sample of children learning Dutch. Methods: Children (MAGE = 71 months) were assigned to a monolingual group with typical development (TD) (n = 30), bilingual TD (n = 30), monolingual LI (n = 30) or bilingual LI group (n = 30). Vocabulary was measured with the Peabody Picture Vocabulary Test, morphology with the Taaltoets Alle Kinderen, verbal short-term (VSTM) and working memory (VWM) with forward and backward digit span tasks. Results: Language knowledge (vocabulary, morphology) was affected by LI and bilingualism. Language processing (VSTM, VWM) was influenced by LI only. When language knowledge was controlled, the bilinguals outperformed the monolinguals on VSTM and VWM when TD and LI were collapsed. Bilingualism aggravated the effects of LI for vocabulary. Conclusions: Bilingualism may create a risk for the vocabulary knowledge of children with LI, but might be beneficial for their verbal memory.
Recent progress in microstructural hydrogen mapping in steels: Quantification, kinetic analysis, and multi-scale characterisation
Authors: Koyama Motomichi , Rohwerder Michael , Tasan Cemal Cem , Bashir Asif , Akiyama Eiji , Takai Kenichi , Raabe Dierk , Tsuzaki Kaneaki
Published: March 2017

This paper gives an overview of recent progress in microstructure-specific hydrogen mapping techniques. The challenging nature of mapping hydrogen with high spatial resolution, i.e. at the scale of finest microstructural features, led to the development of various methodologies: thermal desorption spectrometry, silver decoration, the hydrogen microprint technique, secondary ion mass spectroscopy, atom probe tomography, neutron radiography, and the scanning Kelvin probe. These techniques have different characteristics regarding spatial and temporal resolution associated with microstructure-sensitive hydrogen detection. Employing these techniques in a site-specific manner together with other microstructure probing methods enables multi-scale, quantitative, three-dimensional, high spatial, and kinetic resolution hydrogen mapping, depending on the specific multi-probe approaches used. Here, we present a brief overview of the specific characteristics of each method and the progress resulting from their combined application to the field of hydrogen embrittlement.

This paper is part of a thematic issue on Hydrogen in Metallic Alloys
Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions
Authors: Wu Steven H , Schwartz Rachel S , Winter David J , Conrad Donald F , Cartwright Reed A
Published: March 2017

Motivation

Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others.

Results

We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls.

Availability and Implementation

Methods and data files are available at https://github.com/CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858).

Supplementary information

Supplementary data is available at Bioinformatics online.
Science in the cloud (SIC): A use case in MRI connectomics
Authors: Kiar Gregory , Gorgolewski Krzysztof J. , Kleissas Dean , Roncal William Gray , Litt Brian , Wandell Brian , Poldrack Russel A. , Wiener Martin , Vogelstein R. Jacob , Burns Randal , Vogelstein Joshua T.
Published: March 2017

Modern technologies are enabling scientists to collect extraordinary amounts of complex and sophisticated data across a huge range of scales like never before. With this onslaught of data, we can allow the focal point to shift from data collection to data analysis. Unfortunately, lack of standardized sharing mechanisms and practices often make reproducing or extending scientific results very difficult. With the creation of data organization structures and tools that drastically improve code portability, we now have the opportunity to design such a framework for communicating extensible scientific discoveries. Our proposed solution leverages these existing technologies and standards, and provides an accessible and extensible model for reproducible research, called ‘science in the cloud' (SIC). Exploiting scientific containers, cloud computing, and cloud data services, we show the capability to compute in the cloud and run a web service that enables intimate interaction with the tools and data presented. We hope this model will inspire the community to produce reproducible and, importantly, extensible results that will enable us to collectively accelerate the rate at which scientific breakthroughs are discovered, replicated, and extended.
Disentangling the relative merits and disadvantages of parentage analysis and assignment tests for inferring population connectivity
Authors: Christie Mark R. , Meirmans Patrick G. , Gaggiotti Oscar E. , Toonen Robert J. , White Crow
Published: March 2017

Accurately estimating patterns of population connectivity in marine systems remains an elusive goal. Current genetic approaches have focused on assigning individuals back to their natal populations using one of two methods: parentage analyses and assignment tests. Each of these approaches has their relative merits and weaknesses. Here, we illustrate these tradeoffs using a forward-time agent-based model that incorporates relevant natural history and physical oceanography for 135 Kellet’s whelk (Kelletia kelletii) populations from Southern California. Like most marine organisms, Kellet’s whelks live in large meta-populations where local populations are connected by dispersive larvae. For estimating population connectivity, we found parentage analyses to be relatively insensitive to the amount of genetic differentiation among local populations, but highly sensitive to the proportion of the meta-population sampled. Assignment tests, on the other hand, were relatively insensitive to the proportion of the meta-population sampled, but highly sensitive to the amount of genetic differentiation found among local populations. Comparisons between the true connectivity matrices (generated by using the true origin of all sampled individuals) and those obtained via parentage analyses and assignment tests reveal that neither approach can explain >26% of the variation in true connectivity. Furthermore, even with perfect assignment of all sampled individuals, sampling error alone can introduce noise into the estimated population connectivity matrix. Future work should aim to improve the number of correct assignments without the expense of additional incorrect assignments, perhaps by using dispersal information obtained from related individuals as priors in a Bayesian framework. These analyses dispel a number of common misconceptions in the field and highlight areas for both future research and methodological improvements.
Quality Programs in Neurosurgery: The Memorial Hermann/University of Texas Experience
Authors: Kim Dong H. , Morales Miriam , Tai Rahil , Hergenroeder Georgene , Shah Chirag , O’Leary Joanna , Harrison Nicole , Edquilang Gabrielle , Paisley Emily , Allen-McBride Enedra , Murphy Allison , Smith Justin , Gormley William , Spielman Amanda
Published: March 2017

The importance of outcome measures is steadily increasing due to the rise of “pay for performance” and the advent of population health. In 2007, a quality initiative was started due to poor performance on rankings such as the University Health Consortium (UHC) report card. Inherent to all such efforts are common challenges: how to engage the providers; how to gather and ensure the accuracy of the data; how to attribute results to individuals; how to ensure permanent improvements. After analysis, a strategy was developed that included an initial focus on 3 metrics (mortality, infection rates, and complications), leadership from practicing neurosurgeons, protocol development and adherence, and subspecialization. In addition, it was decided that the metrics would initially apply to attending physicians only, but that the entire team would need to be involved. Once the fundamental elements were established, the process could be extended to other measures and providers. To support this effort, special information system tools were developed and a support team formed. As the program matured, measured outcomes improved and more metrics were added (to a current total of 48). For example, UHC mortality ratios (observed over expected) decreased by 75%. Infection rates decreased 80%. The program now involves all trainee physicians, advanced practice providers, nurses, and other staff. This paper describes the design, implementation, and results of this effort, and provides a practical guide that may be useful to other groups undertaking similar initiatives.
Systematic Review of Safety and Cost-Effectiveness of Venous Thromboembolism Prophylaxis Strategies in Patients Undergoing Craniotomy for Brain Tumor
Authors: Algattas Hanna , Damania Dushyant , DeAndrea-Lazarus Ian , Kimmell Kristopher T , Marko Nicholas F , Walter Kevin A , Vates G Edward , Jahromi Babak S
Published: March 2017

BACKGROUND

Studies have evaluated various strategies to prevent venous thromboembolism (VTE) in neuro-oncology patients, without consensus.

OBJECTIVE

To perform a systematic review with cost-effectiveness analysis (CEA) of various prophylaxis strategies in tumor patients undergoing craniotomy to determine the safest and most cost-effective prophylaxis regimen.

METHODS

A literature search was conducted for VTE prophylaxis in brain tumor patients. Articles reporting the type of surgery, choice of VTE prophylaxis, and outcomes were included. Safety of prophylaxis strategies was determined by measuring rates of VTE and intracranial hemorrhage. Cost estimates were collected based on institutional data and existing literature. CEA was performed at 30 d after craniotomy, comparing the following strategies: mechanical prophylaxis (MP), low molecular weight heparin with MP (MP+LMWH), and unfractionated heparin with MP (MP+UFH) to prevent symptomatic VTE. All costs were reported in 2016 US dollars.

RESULTS

A total of 34 studies were reviewed (8 studies evaluated LMWH, 12 for MP, and 7 for UFH individually or in combination; 4 studies used LMWH and UFH preoperatively). Overall probability of VTE was 1.49% (95% confidence interval (CI) 0.42-3.72) for MP+UFH, 2.72% [95% CI 1.23-5.15] for MP+LMWH, and 2.59% (95% CI 1.31-4.58) for MP, which were not statistically significant. Compared to a control of MP alone, the number needed to treat for MP+UFH is 91 and 769 for MP+LMWH. The risk of intracranial hemorrhage was 0.26% (95% CI 0.01-1.34) for MP, 0.74% (95% CI 0.09-2.61) for MP+UFH, and 2.72% (95% CI 1.23-5.15) for MP+LMWH, which were also not statistically significant. Compared to MP, the number needed to harm for MP+UFH was 208 and for MP+LMWH was 41. Fifteen studies were included in the final CEA. The estimated cost of treatment was $127.47 for MP, $142.20 for MP+UFH, and $169.40 for MP+LMWH. The average cost per quality-adjusted life-year for different strategies was $284.14 for MP+UFH, $338.39 for MP, and $722.87 for MP+LMWH.

CONCLUSION

Although MP+LMWH is frequently considered the optimal prophylaxis for VTE risk reduction, our model suggests that MP+UFH is the safest and most cost-effective measure to balance VTE and hemorrhage risks in brain tumor patients at lower risk of hemorrhage. MP+LMWH may be more effective for patients at higher risk of VTE.
Integrating the Social Sciences
Authors: Calhoun Craig
Published: March 2017

Distinctions among social science disciplines are historically forged and to some extent intellectually arbitrary. Connecting them is therefore crucial to fully addressing many important intellectual and practical concerns. This chapter analyzes three of the most important movements to shape interdisciplinary social science since World War II: area studies, quantitative methods, and problem-oriented research. All three were influenced by funding, by social change, and by desires to make knowledge practically useful. All three influenced basic as well as applied social science. And all three remained approaches that crosscut the disciplinary structure of social science rather than becoming the bases for new disciplines or academic departments. They remain important in themselves and as exemplars of interdisciplinary intellectual work and influence.
A Field of Its Own
Authors: Jasanoff Sheila
Published: March 2017

This chapter presents science and technology studies (STS) as a new island in a preexisting disciplinary archipelago. As a field, STS combines two strands of work dealing, respectively, with the nature and practices of science and technology (S&T) and the relationships between science, technology, and society. As such, STS research focuses on distinctive objects of inquiry and employs novel discourses and methods. The field confronts three significant barriers to achieving greater intellectual coherence, and institutional recognition. First, it must persuade skeptical scientists and university administrators of the need for a critical perspective on S&T. Second, it must demonstrate that traditional disciplines do not adequately analyze S&T. Third, it has to overcome STS scholars’ reluctance to create intellectual boundaries and membership criteria that appear to exclude innovative work. A generation of scholars with graduate degrees in STS are helping to meet these challenges.
Humane Smart Cities
Authors: Costa Eduardo M. , Oliveira Álvaro D.
Published: March 2017

Humane smart cities is a new field of study that addresses what has to be done in cities to make them more livable and more in tune with their citizen’s wishes and needs. The concept is different from the existing smart city concept. The latter focuses on technology as the main driver of change. Humane smart cities use all the power of technology but only in direct connection with citizens’ needs. Boroughs should contain options for living, working, and playing in the same region. Transport should focus on walking, biking, and public transport rather than cars. Cocreation and close interaction between citizens and City Hall should become the norm. In short, the chapter examines how we can keep the good things we like in the city and avoid the bad ones that were brought about by poor planning and wrong models of urban development.
Interdisciplinary Learning
Authors: Mansilla Veronica Boix
Published: March 2017

This chapter examines cognitive and epistemological foundations of interdisciplinary learning and their implications for quality interdisciplinary instruction. It shows that learning processes conducive to interdisciplinary integration reflect the plurality of interdisciplinary pursuits and disciplinary epistemologies—for example, from creating a historical monument to producing a complex explanation of overfishing. The chapter offers an epistemological framework to understand the cognitive demands of interdisciplinary learning and integration pointing to four processes in dynamic interaction: (1) establishing purpose; (2) weighing disciplinary insights; (3) building leveraging integrations, and (4) maintaining a critical stance. In interdisciplinary learning, such processes interact, informing one another as learning progresses iteratively. The result is a system of thought in reflective equilibrium—an improvement in understanding vis-à-vis prior beliefs, as well as an understanding subject to further revision. The framework is applied to two distinct examples of interdisciplinary work and implications for quality instruction are outlined
Addressing Wicked Problems through Transdisciplinary Research
Authors: Pohl Christian , Truffer Bernhard , Hirsch-Hadorn Gertrude
Published: March 2017

In a number of European countries a particular understanding of transdisciplinarity has evolved over the last decades, initiated by research on environmental problems. The focus of this type of transdisciplinary research is on helping society solve wicked problems. A specific feature is that, in addition to researchers of different disciplines, representatives of civil society and the private and public sectors are involved in the research process. “Addressing Wicked Problems through Transdisciplinary Research” describes this type of transdisciplinary research, its roots, and the challenges to be dealt with when addressing wicked societal problems.
Managing Consensus in Inter- and Transdisciplinary Teams: Tasks and Expertise
Authors: Defila Rico , di Giulio Antonietta
Published: March 2017

Collaborative problem framing is crucial to arrive at integrated results in inter- and transdisciplinary research projects. Its significance is supported by empirical evidence gained in a survey, which shows significant differences concerning common goals, language, and theoretical basis between teams who had achieved a synthesis and those that had not. A shared view of a problem and of how to deal with it is the starting point for inquiries of individuals and/or subprojects, and the point to return to after their results are available. Thus, balancing collaborative and individual work is crucial in managing such projects. Managing inter- or transdisciplinary projects covers a number of highly demanding processes taking place during their life span. It is a complex and demanding scientific task that could be called “content-rich moderation” (following the German “Inhaltsreiche Moderation”) to express its nature. To succeed, managers of inter- or transdisciplinary projects need different kinds of expertise.
Interdisciplinary Pedagogies in Higher Education
Authors: DeZure Debora
Published: March 2017

“Interdisciplinary Pedagogies in Higher Education” explores the increasing integration of goals for interdisciplinary learning in American higher education. The chapter begins with working definitions of interdisciplinary learning and the many factors that have led to its proliferation. It then reviews the elaboration of new methods to teach and to assess interdisciplinary learning, emerging models of interdisciplinary problem-solving, and practice-oriented resources and online tools to assist undergraduate, graduate, and professional students and their instructors with interdisciplinary problem-solving and communications in cross-disciplinary and interprofessional contexts. The chapter concludes with the impact of technology, for example, e-portfolios and other digital and technology-enabled tools, and evidence of an emerging body of scholarship of teaching and learning focused on interdisciplinary learning.
Facilitating Interdisciplinary Scholars
Authors: Pfirman Stephanie , Martin Paula J. S.
Published: March 2017

“Facilitating Interdisciplinary Scholars,” by Stephanie Pfirman and Paula J. S. Martin, explores approaches to interdisciplinary scholarship with comparison to disciplinary traditions in higher education. The authors investigate the particular challenges of interdisciplinary research, teaching, and service for scholars throughout different mileposts in a scholarly career. Ideas to support interdisciplinary faculty are presented, from the creation of the position, to the point of hire, and through a career timeline to tenure and posttenure review. As many institutions have barriers for scholars working between departments, frameworks to foster interdisciplinary collaboration are discussed. Special challenges in interdisciplinary scholarly productivity, scholarly recognition, evaluation, promotion, and funding are examined.
Interdisciplinarity in the Biological Sciences
Authors: Burggren Warren , Chapman Kent , Keller Bradley B. , Monticino Michael , Torday John S.
Published: March 2017

The biological sciences have long benefited from the intellectual and pragmatic input of ideas and techniques from other disciplines, including medicine, chemistry, engineering, and mathematics. “Interdisciplinarity in the Biological Sciences” discusses the synergies that have emerged from the integration of these disciplines into the biological sciences, and uses examples to strongly advocate for such approaches. The reach of biology extends well beyond the sciences and technology into interdisciplinary interactions within the social sciences, arts, and humanities. Finally, interdisciplinary collaboration between various scientists, engineers, and mathematicians is not without its pitfalls and impediments, from both an individual and institutional perspective, so some potential hurdles to effective interdisciplinary research are outlined.
Thucydides and His Intellectual Milieu
Authors: Thomas Rosalind
Published: March 2017

The chapter examines Thucydides’ intellectual milieu, concentrating on medical theories of the time, rhetoric, and especially the rhetorical use of theories of justice and self-interest. It examines the account of the Plague and the impossibility of isolating a cause, akribeia as a wider aim of medical writers, and Thucydides’ familiarity with intellectual theories, which he then supersedes. Finally, it examines aspects of the presentation of rhetoric and its effects: it focuses on Thucydides’ Plataean Debate and the claims made to justice, law, and convention, comparing Antiphon and Thrasymachus’ theories of justice and Thucydides’ possible contribution to this debate.