bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligodendrocytes contribute to motor neuron death in ALS via SOD1-dependent mechanism
Authors: Ferraiuolo Laura , Meyer Kathrin , Sherwood Thomas W. , Vick Jonathan , Likhite Shibi , Frakes Ashley , Miranda Carlos J. , Braun Lyndsey , Heath Paul R. , Pineda Ricardo , Beattie Christine E. , Shaw Pamela J. , Askwith Candice C. , McTigue Dana , Kaspar Brian K. 
Published: September 2016

Significance
Oligodendrocytes have been implicated in disease pathology in amyotrophic lateral sclerosis (ALS) using transgenic mouse models. To date there is no human coculture system available to investigate oligodendrocyte involvement in motor neuron (MN) death in ALS. Our data highlight that oligodendrocytes derived from patients with familial and sporadic ALS from induced pluripotent stem cells and induced neural progenitor cells play an active role in MN death. Oligodendrocyte toxicity is mediated through soluble factors and cell-to-cell contact, thus identifying multiple mechanisms of action and therapeutic opportunities. Their pathogenic phenotype can be reversed by achieving superoxide dismutase 1 knockdown in early oligodendrocyte progenitors in both familial and sporadic cases, but not chromosome 9 ORF 72 samples. This study provides important insights for patient subgrouping and timelines for therapeutic approaches.
Targeted imaging of urothelium carcinoma in human bladders by an ICG pHLIP peptide ex vivo
Authors: Golijanin Jovana , Amin Ali , Moshnikova Anna , Brito Joseph M. , Tran Timothy Y. , Adochite Ramona-Cosmina , Andreev Gregory O. , Crawford Troy , Engelman Donald M. , Andreev Oleg A. , Reshetnyak Yana K. , Golijanin Dragan 
Published: September 2016

Significance
Bladder cancer is the fifth most common cancer. Timely diagnosis and appropriate early management protocols are of paramount significance for improving patient outcomes. This study shows efficient pH-dependent near-infrared imaging of bladder malignant tumors without targeting of normal tissue. Our results demonstrate that the indocyanine green pH low insertion peptide (pHLIP) construct is suitable for use as a predictive clinical marker, specifically staining human bladder tumors after intravesical administration ex vivo. The targeting allows delivery of various imaging probes, which may offer early diagnosis and improve the outcomes of endoscopic and radical surgical resection of urothelial carcinomas. In addition, delivery of therapeutic molecules to cancer cells by pHLIP might open an opportunity for novel targeted treatment of bladder cancers.
Transferable model for chromosome architecture
Authors: Di Pierro Michele , Zhang Bin , Aiden Erez Lieberman , Wolynes Peter G. , Onuchic José N. 
Published: September 2016

Significance
Chromatin consists of DNA and hundreds of proteins that interact with the genetic material. In vivo, chromatin folds into nonrandom structures. The physical mechanism leading to these characteristic conformations, however, remains poorly understood. Here, we introduce a model that generates chromosome conformations by using the idea that chromatin can be subdivided into types based on its biochemical interactions. Chromatin types, which are distinct from DNA sequence, are partially epigenetically controlled and change during cell differentiation, thus constituting a link between epigenetics, chromosomal organization, and cell development. The degree of accuracy achieved by this model supports the viability of the proposed physical mechanism of chromatin folding and makes the computational model a powerful tool for future investigations.
Cisplatin DNA damage and repair maps of the human genome at single-nucleotide resolution
Authors: Hu Jinchuan , Lieb Jason D. , Sancar Aziz , Adar Sheera 
Published: September 2016

Significance
The chemotherapy drug cisplatin kills cancer cells by damaging their DNA. It has been used for treating a variety of cancer types for almost four decades. Although the drug is generally effective, it has strong adverse side effects, and some cancers exhibit or, after initial favorable response, develop drug resistance. The mechanism of drug resistance is multifactorial and involves the ability of cancer cells to repair the cisplatin-induced DNA damages. We have developed methods to map the sites of cisplatin damage and its repair for the entire human genome at single-nucleotide resolution. These methods can be used to study cancer sensitivity and resistance to the drugs, and to identify new strategies for efficient combination therapies.
Ultralight or Heavyweight? The Interactive Effects of Gear Strength and Air Exposure on Reflex Impairment in Largemouth Bass
Authors: Cooke S. J. , Cooke C. J. A. , Brownscombe J. W. 
Published: September 2016

AbstractAlthough much is known about the factors that influence the effects of catch‐and‐release angling on fish condition and survival, relatively little is known about the effects of fishing gear strength on fight time and, hence, fish condition. Moreover, little is known about how gear strength and fight time interact with air exposure duration to ultimately influence the level of exhaustion experienced by fish at time of release. Here we systematically varied fishing gear strength (ultralight versus medium‐heavy) and air exposure duration (0 versus 120 s) when targeting Largemouth Bass Micropterus salmoides. We relied on reflex impairment (using five different reflexes) as a real‐time indicator of fish condition. Largemouth Bass fight durations were highly variable between fishing gear types and across fish sizes. Largemouth Bass captured on ultralight fishing gear experienced longer fight times, and there was a stronger positive relationship between fish length and fight time than for those captured on heavier fishing gear. However, fish captured using ultralight gear were easier to handle upon landing and thus experienced shorter hook removal times, which may result in less air exposure in actual angling scenarios. Fish captured with ultralight gear had significantly higher reflex impairment than those captured with heavy gear with no air exposure, while fish captured with both gear types had similarly high reflex impairment when exposed to the air. These results indicate that gear strength does influence the level of exhaustion experienced by Largemouth Bass. However, fish that are landed quickly are so vigorous that handling and hook removal are challenging. We submit that there is likely a compromise where neither ultralight nor ultraheavy gear (always relative to the size and species targeted) is appropriate. Moreover, our findings emphasize the importance of minimizing air exposure, particularly for fish that are exhausted already from a protracted fight.Received December 29, 2015; accepted June 24, 2016 Published online September 30, 2016
Brook Trout, Brown Trout, and Ectoparasitic CopepodsSalmincola edwardsii: Species Interactions as a Proximate Cause of Brook Trout Loss Under Changing Environmental Conditions
Authors: Mitro Matthew G. 
Published: September 2016

AbstractChanges in environmental conditions are expected to affect stream temperature and ultimately the presence of native Brook TroutSalvelinus fontinalisin Wisconsin streams. While change in climate may be an ultimate cause of Brook Trout loss, proximate causes may involve factors other than intolerance to high temperatures. Here I present data to support the hypothesis that species interactions among Brook Trout, naturalized Brown TroutSalmo trutta, and ectoparasitic copepodsSalmincola edwardsiiin the context of changing environmental conditions can lead to declines in Brook Trout recruitment and abundance. WhileS. edwardsiiare endemic to Wisconsin streams and infect Brook Trout, they do not infect Brown Trout.Salmincola edwardsiiwere first documented in Ash Creek, Wisconsin, in 2010 and became epizootic in 2012. Conditions in 2012 conducive to an epizootic included anomalously warm stream temperatures, relative drought conditions, and an increasing sympatric population of Brown Trout. Infection prevalence increased from 42% in April 2012 to 95% in October. Average intensity of infection in 2012 was 5.5 copepods per age‐0 Brook Trout and 16.1 per Brook Trout age 1 and older. Variation in Brook Trout recruitment appeared to be related to stock size and environmental factors, including flood events, Brown Trout abundance, andS. edwardsiiepizootics. In 2012, flow conditions were conducive to salmonid recruitment, but Brook Trout recruitment fell precipitously relative to that of Brown Trout. Recruitment of age‐0 Brook Trout duringS. edwardsiiepizootics in 2012–2014 decreased about 77% and 89% compared with recruitment in 2007–2011 and 2005–2006, respectively. Following three consecutive years ofS. edwardsiiepizootics and poor recruitment, Brook Trout were nearing extirpation from Ash Creek. The data support the hypothesis that species interactions among fish and an ectoparasitic copepod under stressful environmental and ultimately climatic conditions can be a proximate cause of native Brook Trout loss.Received February 15, 2016; accepted July 28, 2016 Published online September 30, 2016
Effects of Air Exposure on Postrelease Mortality Rates of White Marlin Caught in the U.S. Offshore Recreational Fishery
Authors: Graves John E. , Marcek Benjamin J. , Goldsmith William M. 
Published: September 2016

Abstract
White Marlin Kajikia albida are targeted by recreational fisheries in tropical and subtropical waters of the Atlantic Ocean. Off the U.S. East Coast, the vast majority of White Marlin are released after capture. Federal regulations prohibit anglers from removing a White Marlin from the water unless the fish is to be retained; however, numerous photographs of anglers holding White Marlin out of the water are posted on the Internet each summer, demonstrating that there is considerable noncompliance with this management measure. To better understand the effect of air exposure on postrelease survival of White Marlin, we attached pop-up satellite archival tags (PSATs; programmed to release after 30 d) to individuals that were caught on natural baits rigged with circle hooks and that were removed from the water for a period of 1 min (n = 6 fish), 3 min (n = 5 fish), or 5 min (n = 7 fish). We compared our results with those from a previous study in which PSATs were used to follow the fates of 59 White Marlin that were caught on circle hooks but not removed from the water. The proportion of postrelease mortalities increased with air exposure duration; the overall rate of postrelease mortality was significantly higher for White Marlin that were subjected to air exposure (33.3%) than for those that remained in the water (1.7%). These data provide strong support for the current U.S. regulation prohibiting the removal of a White Marlin from the water if the fish is to be released. Effective communication of the deleterious effects of air exposure on White Marlin should help to deter the practice of removing fish from the water among members of the recreational angling community, which has been supportive of other conservation measures for this species.
Received January 13, 2016; accepted June 15, 2016 Published online September 30, 2016
Control of power, torque, and instability drive using in-shot variable neutral beam energy in tokamaks
Authors: Pace D.C. , Collins C.S. , Crowley B. , Grierson B.A. , Heidbrink W.W. , Pawley C. , Rauch J. , Scoville J.T. , Van Zeeland M.A. , Zhu Y.B. 
Published: September 2016

Abstract
A first-ever demonstration of controlling power and torque injection through time evolution of neutral beam energy has been achieved in recent experiments at the DIII-D tokamak (Luxon 2002 Nucl. Fusion
42 614). Pre-programmed waveforms for the neutral beam energy produce power and torque inputs that can be separately and continuously controlled. Previously, these inputs were tailored using on/off modulation of neutral beams resulting in large perturbations (e.g. power swings of over 1 MW). The new method includes, importantly for experiments, the ability to maintain a fixed injected power while varying the torque. In another case, different beam energy waveforms (in the same plasma conditions) produce significant changes in the observed spectrum of beam ion-driven instabilities. Measurements of beam ion loss show that one energy waveform results in the complete avoidance of coherent losses due to Alfvénic instabilities. This new method of neutral beam operation is intended for further application in a variety of DIII-D experiments including those concerned with high-performance steady state scenarios, fast particle effects, and transport in the low torque regime. Developing this capability would provide similar benefits and improved plasma control for other magnetic confinement fusion facilities.
Global kinetic ballooning mode simulations in BOUT++
Authors: Ma C.H. , Xu X.Q. 
Published: September 2016

Abstract
We report on simulation results of a 3+1 gyro-Landau-fluid (GLF) model in BOUT++ framework, which contributes to increasing the physics understanding of the edge turbulence. We find that there is no second stability region of kinetic ballooning modes (KBM) in the concentric circular geometry. The first unstable β of KBM decreases below the ideal ballooning mode threshold with increasing

η

i

. In order to study the KBM in the real tokamak equilibrium, we find that the approximation of shifted circular geometry (

β
≪

ε

2

) is not valid for a high β global equilibrium near the second stability region of KBM. Thus we generate a series of real equilibria from a global equilibrium solver CORSICA, including both Shafranov shift and elongation effects, but not including bootstrap current. In these real equilibria, the second stability region of KBM are observed in our global linear simulations. The most unstable mode for different β are the same while the mode number spectrum near the second stability region is wider than the case near the first stability region. The nonlinear simulations show that the energy loss of an ELM keeps increasing with β, because the linear drive of the turbulence remains strong for the case near the second stability region during profile evolution.
NIMROD modeling of quiescent H-mode: reconstruction considerations and saturation mechanism
Authors: King J.R. , Burrell K.H. , Garofalo A.M. , Groebner R.J. , Kruger S.E. , Pankin A.Y. , Snyder P.B. 
Published: September 2016

Abstract
The extended-MHD NIMROD code (Sovinec and King 2010 J. Comput. Phys. 229 5803) models broadband-MHD activity from a reconstruction of a quiescent H-mode shot on the DIII-D tokamak (Luxon 2002 Nucl. Fusion
42 614). Computations with the reconstructed toroidal and poloidal ion flows exhibit low-

n

ϕ

perturbations (

n

ϕ

≃
1

–5) that grow and saturate into a turbulent-like MHD state. The workflow used to project the reconstructed state onto the NIMROD basis functions re-solves the Grad–Shafranov equation and extrapolates profiles to include scrape-off-layer currents. Evaluation of the transport from the turbulent-like MHD state leads to a relaxation of the density and temperature profiles.
On the width of a pedestal in the H-mode
Authors: Itoh K. , Itoh S.-I. , Kamiya K. , Kobayashi T. 
Published: September 2016

Abstract
The thickness of the transport barrier at the plasma edge is discussed, by analyzing the structure of the interface region between the turbulent L-mode region and the region where the transport is strongly-stabilized by the electric field. The effect of this localized radial electric field is prescribed. The spatial profile of turbulence intensity is analyzed by using a simplified model, in which the suppression and transport of turbulence intensity are introduced. The scaling property of the transport barrier is discussed.
Impact of zonal flows on edge pedestal collapse
Authors: Jhang Hogun , Kaang Helen H. , Kim S.S. , Rhee T. , Singh R. , Hahm T.S. 
Published: September 2016

Abstract
We perform a computational study of the role of zonal flows in edge pedestal collapse on the basis of a nonlinear three-field reduced magnetohydrodynamic (MHD) model. A dramatic change of dynamics takes place when ideal ballooning modes are completely stabilized. Analyses show that a new instability is developed due to a strong excitation of zonal vorticity, resulting in a series of secondary crashes. The presence of subsidiary bursts after a main crash increases the effective crash time and energy loss. These simulation results resemble the behavior of compound edge localized modes (ELMs). Analyses in this paper indicate that a complete understanding of ELM crash dynamics requires the self-consistent inclusion of nonlinear zonal flows-MHD interaction and transport physics.
Gyrokinetic study of turbulent convection of heavy impurities in tokamak plasmas at comparable ion and electron heat fluxes
Authors: Angioni C. , Bilato R. , Casson F.J. , Fable E. , Mantica P. , Odstrcil T. , Valisa M. 
Published: September 2016

Abstract
In tokamaks, the role of turbulent transport of heavy impurities, relative to that of neoclassical transport, increases with increasing size of the plasma, as clarified by means of general scalings, which use the ITER standard scenario parameters as reference, and by actual results from a selection of discharges from ASDEX Upgrade and JET. This motivates the theoretical investigation of the properties of the turbulent convection of heavy impurities by nonlinear gyrokinetic simulations in the experimentally relevant conditions of comparable ion and electron heat fluxes. These conditions also correspond to an intermediate regime between dominant ion temperature gradient turbulence and trapped electron mode turbulence. At moderate plasma toroidal rotation, the turbulent convection of heavy impurities, computed with nonlinear gyrokinetic simulations, is found to be directed outward, in contrast to that obtained by quasi-linear calculations based on the most unstable linear mode, which is directed inward. In this mixed turbulence regime, with comparable electron and ion heat fluxes, the nonlinear results of the impurity transport can be explained by the coexistence of both ion temperature gradient and trapped electron modes in the turbulent state, both contributing to the turbulent convection and diffusion of the impurity. The impact of toroidal rotation on the turbulent convection is also clarified.
Impact of ion diamagnetic drift on MHD stability at edge pedestal in JT-60U rotating plasmas
Authors: Aiba N. , Honda M. , Kamiya K. 
Published: September 2016

Abstract
The effect of ion diamagnetic drift on the stability of peeling–ballooning modes in rotating tokamak plasmas has been analyzed numerically. The results show that plasma toroidal rotation can not only destabilize the peeling–ballooning mode but also can reduce the ion diamagnetic drift effect on the mode stability, even though the ion diamagnetic drift effect stabilizes the mode in a static plasma. Plasma poloidal rotation can also destabilize the mode and cancel the ion diamagnetic drift effect, even when the rotation frequency is much smaller than the toroidal one. These impacts of the rotation on the stability can resolve the discrepancy between the result of the numerical stability analysis and the experimental result in type-I ELMy H-mode plasmas in JT-60U. The reduction of the ion diamagnetic drift effect on ELM stability due to plasma rotation is shown to depend on the direction of the rotation, so that the ion diamagnetic drift effect becomes negligible only when the JT-60U plasma rotates in the direction counter to the plasma current.
Anomalous transport in the H-mode pedestal of Alcator C-Mod discharges
Authors: Pankin A.Y. , Hughes J.W. , Greenwald M.J. , Kritz A.H. , Rafiq T. 
Published: September 2016

Abstract
Anomalous transport in the H-mode pedestal region of five Alcator C-Mod discharges, representing a collisionality scan is analyzed. The understanding of anomalous transport in the pedestal region is important for the development of a comprehensive model for the H-mode pedestal slope. In this research, a possible role of the drift resistive inertial ballooning modes (Rafiq et al 2010 Phys. Plasmas
17 082511) in the edge of Alcator C-Mod discharges is analyzed. The stability analysis, carried out using the TRANSP code, indicates that the DRIBM modes are strongly unstable in Alcator C-Mod discharges with large electron collisionality. An improved interpretive analysis of H-mode pedestal experimental data is carried out utilizing the additive flux minimization technique (Pankin et al 2013 Phys. Plasmas
20 102501) together with the guiding-center neoclassical kinetic XGC0 code. The neoclassical and neutral physics are simulated in the XGC0 code and the anomalous fluxes are computed using the additive flux minimization technique. The anomalous fluxes are reconstructed and compared with each other for the collisionality scan Alcator C-Mod discharges. It is found that the electron thermal anomalous diffusivities at the pedestal top increase with the electron collisionality. This dependence can also point to the drift resistive inertial ballooning modes as the modes that drive the anomalous transport in the plasma edge of highly collisional discharges.
Non-linear modeling of the plasma response to RMPs in ASDEX Upgrade
Authors: Orain F. , Hölzl M. , Viezzer E. , Dunne M. , Bécoulet M. , Cahyna P. , Huijsmans G.T.A. , Morales J. , Willensdorfer M. , Suttrop W. , Kirk A. , Pamela S. , Günter S. , Lackner K. , Strumberger E. , Lessig A. 
Published: September 2016

Abstract
The plasma response to resonant magnetic perturbations (RMPs) in ASDEX Upgrade is modeled with the non-linear resistive MHD code JOREK, using input profiles that match those of the experiments as closely as possible. The RMP configuration for which edge localized modes are best mitigated in experiments is related to the largest edge kink response observed near the X-point in modeling. On the edge resonant surfaces q  =  m/n, the coupling between the kink component (m  >  nq) and the m resonant component is found to induce the amplification of the resonant magnetic perturbation. The ergodicity and the 3D-displacement near the X-point induced by the resonant amplification can only partly explain the density pumpout observed in experiments.
Selected transport studies of a tokamak-based DEMO fusion reactor
Authors: Fable E. , Wenninger R. , Kemp R. 
Published: September 2016

Abstract
As a next-step in the tokamak-based fusion programme, the DEMO fusion reactor is foreseen to produce relevant output electricity, in the order of  ∼500 MW delivered to the network. The scenarios that are being presently investigated consist of a pulsed device, called DEMO1, and a steady-state device, called DEMO2. In this work, which is focused on the pulsed device DEMO1, scenarios are studied from the point of view of core transport, to assess plasma performance and limitations due to core microinstabilities. The role of radiated power, aspect ratio, and height of temperature pedestal are assessed as they impact both core energy and particle transport. Open issues in this framework are also discussed.