bluuebunny/crossref_metadata_2025 huggingface dataset:
Phytoplankton light absorption and the package effect in relation to photosynthetic and photoprotective pigments in the northern tip of Antarctic Peninsula
Authors: Ferreira Amabile , Ciotti Áurea M. , Mendes Carlos Rafael B. , Uitz Julia , Bricaud Annick
Published: August 2017

This study investigates the variability in the spectral absorption of phytoplankton in Antarctic waters. A large in situ data set comprising phytoplankton pigments and hyperspectral absorption was measured in the northern tip of Antarctic Peninsula during 2013 and 2014 summers at several depths. A proxy of package effect was estimated from the phytoplankton absorption spectra, independently of chlorophyll a. Variations in the concentration of photosynthetic and photoprotective pigments were discernible by changes in this metric but not in the chlorophyll a specific absorption coefficient of phytoplankton. The fucoxanthin to chlorophyll a ratio correlated positively to package effect due to an increase in cell size of phytoplankton (diatoms) and increasing fucoxanthin content per cell to maximize light harvesting in depth. The package effect was found to covary inversely with photoprotective pigments relative to chlorophyll a, partially due to their contribution to enhance absorption in the blue part of the spectrum. Using a cluster analysis (k‐means algorithm) on the phytoplankton absorption spectra, we illustrate the capacity to identify a regular increase in the degree of package effect. This approach can be useful to classify the phytoplankton assemblages in Antarctic waters according to different degrees of pigment packaging, each one related to a specific pigment composition. Our results demonstrate the potential for this classification at different temporal and spatial scales from ocean color satellite data. This should improve our understanding of deviations in global bio‐optical algorithms when applied to the Southern Ocean.
Geometry of a large‐scale, low‐angle, midcrustal thrust (Woodroffe Thrust, central Australia)
Authors: Wex S. , Mancktelow N. S. , Hawemann F. , Camacho A. , Pennacchioni G.
Published: August 2017

The Musgrave Block in central Australia exposes numerous large‐scale mylonitic shear zones developed during the intracontinental Petermann Orogeny around 560–520 Ma. The most prominent structure is the crustal‐scale, over 600 km long, E‐W trending Woodroffe Thrust, which is broadly undulate but generally dips shallowly to moderately to the south and shows an approximately top‐to‐north sense of movement. The estimated metamorphic conditions of mylonitization indicate a regional variation from predominantly midcrustal (circa 520–620°C and 0.8–1.1 GPa) to lower crustal (~650°C and 1.0–1.3 GPa) levels in the direction of thrusting, which is also reflected in the distribution of preserved deformation microstructures. This variation in metamorphic conditions is consistent with a south dipping thrust plane but is only small, implying that a ≥60 km long N‐S segment of the Woodroffe Thrust was originally shallowly dipping at an average estimated angle of ≤6°. The reconstructed geometry suggests that basement‐cored, thick‐skinned, midcrustal thrusts can be very shallowly dipping on a scale of many tens of kilometers in the direction of movement. Such a geometry would require the rocks along the thrust to be weak, but field observations (e.g., large volumes of syntectonic pseudotachylyte) argue for a strong behavior, at least transiently. Localization on a low‐angle, near‐planar structure that crosscuts lithological layers requires a weak precursor, such as a seismic rupture in the middle to lower crust. If this was a single event, the intracontinental earthquake must have been large, with the rupture extending laterally over hundreds of kilometers.
One‐Pot Synthesis of Functionalized Holey Graphene/Sulfur Composite for Lithium–Sulfur Batteries
Authors: Chang Ni , Zhou Chungen , Fu Hao , Zhao Yan , Shui Jianglan
Published: August 2017

Lithium–sulfur (Li–S) batteries are promising energy storage devices owing to their high theoretical energy density and environmental friendliness. However, drawbacks such as poor conductivity of element sulfur, “shuttle effect,” and serious volume expansion hinder the application of Li–S batteries. Herein, this paper reports a functionalized holey graphene/sulfur composite fabricated by a facile one‐pot synthesis method as the cathode for Li–S batteries. The uniformly and densely distributed microholes are etched out on graphene sheets by H2O2 oxidation, with the tunable hole‐ size and the oxygen‐functional group doping along the hole‐edge. The numerous microholes serve as the fast pathways for ions through the graphene sheets, while the polar oxygen‐functional groups inhibit the movement of lithium polysulfides. Such a functionalized holey graphene/sulfur composite with the optimal hole‐size of 0.6 nm shows a significantly enhanced electrochemical performance compared with the control sample without the microholes or functional groups.
Cellulose Nanocrystal:Polymer Hybrid Optical Diffusers for Index‐Matching‐Free Light Management in Optoelectronic Devices
Authors: Mahpeykar Seyed Milad , Zhao Yongbiao , Li Xiyan , Yang Zhenyu , Xu Qiwei , Lu Zheng‐Hong , Sargent Edward H. , Wang Xihua
Published: August 2017

A novel optical diffuser based on cellulose nanocrystals (CNCs) embedded in polydimethylsiloxane (PDMS) matrix, or cellulose nanocrystal:polymer (CNP) is reported. By offering simple low‐cost fabrication process as well as compatibility with large‐scale production, the proposed optical diffuser is a better choice for integration into optoelectronic devices for light management compared to other cellulose‐based diffusers due to its physical durability and the lack of requirement for index‐matching between the diffuser and the optoelectronic device thanks to the unique surface properties, mechanical flexibility, and optical transparency offered by PDMS as the matrix material. It is demonstrated that CNCs are an excellent filler material to pair up with PDMS in an optical diffuser providing highly efficient broadband light diffusion in visible and near‐infrared range of light at very low concentrations (≈1 wt%). At its optimized form, a CNP hybrid optical diffuser is capable of achieving very high haze values (up to 85%) while maintaining a high degree of transparency (≈85%) at the same time. As a proof of concept, light management capabilities of CNP hybrid optical diffusers are leveraged to demonstrate their potential for light extraction improvement in organic light‐emitting diodes and light absorption enhancement in thin‐film solar cells.
Copper‐Catalyzed C−H Activation of Substituted Pyridines Leading to Imidazopyridine Derivatives via Self‐Redox of the Substrates
Authors: Lou Zhenbang , Yang Haijun , Zhu Changjin , Fu Hua
Published: August 2017

A simple and practical copper‐catalyzed C−H activation of substituted pyridines with O‐aryl oximes leading to imidazo[1,2‐a]pyridines has been developed via self‐redox of the substrates. The reaction performed well under mild conditions, tolerating many functional groups. Importantly, the C−H activation did not need an added oxidant, additive, acid or base.
An E‐HOIM Based Data‐Driven Adaptive TILC of Nonlinear Discrete‐Time Systems for Non‐Repetitive Terminal Point Tracking
Authors: Lin Na , Chi Ronghu , Huang Biao , Chien Chiang‐Ju , Feng Yuanjing
Published: August 2017

This work proposes a new adaptive terminal iterative learning control approach based on the extended concept of high‐order internal model, or E‐HOIM‐ATILC, for a nonlinear non‐affine discrete‐time system. The objective is to make the system state or output at the endpoint of each operation track a desired target value. The target value varies from one iteration to another. Before proceeding to the data‐driven design of the proposed approach, an iterative dynamical linearization is performed for the unknown nonlinear systems by using the gradient of the nonlinear system with regard to the control input as the iteration‐and‐time‐varying parameter vector of the equivalent linear I/O data model. By virtue of the basic idea of the internal model, the inverse of the parameter vector is approximated by a high‐order internal model. The proposed E‐HOIM‐ATILC does not use measurements of any intermediate points except for the control input and terminal output at the endpoint. Moreover, it is data‐driven and needs merely the terminal I/O measurements. By incorporating additional control knowledge from the known portion of the high order internal model into the learning control law, the control performance of the proposed E‐HOIM‐ATILC is improved. The convergence is shown by rigorous mathematical proof. Simulations through both a batch reactor and a coupled tank system demonstrate the effectiveness of the proposed method.
High yield process for the production of active human α‐galactosidase a in CHO‐K1 cells through lentivirus transgenesis
Authors: Rodríguez María Celeste , Ceaglio Natalia , Antuña Sebastián , Tardivo María Belén , Etcheverrigaray Marina , Prieto Claudio
Published: August 2017

Fabry disease is an X‐linked recessive disorder caused by a deficiency in lysosomal α‐Galactosidase A. Currently, two enzyme replacement therapies (ERT) are available. However, access to orphan drugs continues to be limited by their high price. Selection of adequate high‐expression systems still constitutes a challenge for alleviating the cost of treatments. Several strategies have been implemented, with varying success, trying to optimize the production process of recombinant human α‐Galactosidase A (rhαGAL) in Chinese hamster ovary (CHO‐K1) cells. Herein, we describe for the first time the application of a strategy based on third‐generation lentiviral particles (LP) transduction of suspension CHO‐K1 cells to obtain high‐producing rhαGAL clones (3.5 to 59.4 pg cell−1 d−1). After two purification steps, the active enzyme was recovered (2.4 × 106 U mg−1) with 98% purity and 60% overall yield. Michaelis‐Menten analysis demonstrated that rhαGAL was capable of hydrolyzing the synthetic substrate 4MU‐α‐Gal at a comparable rate to Fabrazyme®, the current CHO‐derived ERT available for Fabry disease. In addition, rhαGAL presented the same mannose‐6‐phosphate (M6P) content, about 40% higher acid sialic amount and 33% reduced content of the immunogenic type of sialic acid (Neu5Gc) than the corresponding ones for Fabrazyme®. In comparison with other rhαGAL production processes reported to date, our approach achieves the highest rhαGAL productivity preserving adequate activity and glycosylation pattern. Even more, considering the improved glycosylation characteristics of rhαGAL, which might provide advantages regarding pharmacokinetics, our enzyme could be postulated as a promising alternative for therapeutic use in Fabry disease. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1334–1345, 2017
Isotope labeling to determine the dynamics of metabolic response in CHO cell perfusion bioreactors using MALDI‐TOF‐MS
Authors: Karst Daniel J. , Steinhoff Robert F. , Kopp Marie R. G. , Soos Miroslav , Zenobi Renato , Morbidelli Massimo
Published: August 2017

The steady‐state operation of Chinese hamster ovary (CHO) cells in perfusion bioreactors requires the equilibration of reactor dynamics and cell metabolism. Accordingly, in this work we investigate the transient cellular response to changes in its environment and their interactions with the bioreactor hydrodynamics. This is done in a benchtop perfusion bioreactor using MALDI‐TOF MS through isotope labeling of complex intracellular nucleotides (ATP, UTP) and nucleotide sugars (UDP‐Hex, UDP‐HexNAc). By switching to a 13C6 glucose containing feed media during constant operation at 20 × 106 cells and a perfusion rate of 1 reactor volume per day, isotopic steady state was studied. A step change to the 13C6 glucose medium in spin tubes allowed the determination of characteristic times for the intracellular turnover of unlabeled metabolites pools,
(≤0.56 days), which were confirmed in the bioreactor. On the other hand, it is shown that the reactor residence time
(1 day) and characteristic time for glucose uptake
(0.33 days), representative of the bioreactor dynamics, delayed the consumption of 13C6 glucose in the bioreactor and thus the intracellular 13C enrichment. The proposed experimental approach allowed the decoupling of bioreactor hydrodynamics and intrinsic dynamics of cell metabolism in response to a change in the cell culture environment. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1630–1639, 2017
Bacterial community analysis in upflow multilayer anaerobic reactor treating high‐solids organic wastes
Authors: Cho Si‐Kyung , Jung Kyung‐Won , Kim Dong‐Hoon , Kwon Joong‐Chun , Ijaz Umer Zeeshan , Shin Seung Gu
Published: August 2017

A novel anaerobic digestion configuration, the upflow multi‐layer anaerobic reactor (UMAR), was developed to treat high‐solids organic wastes. The UMAR was hypothesized to form multi‐layer along depth due to the upflow plug flow; use of a recirculation system and a rotating distributor and baffles aimed to assist treating high‐solids influent. The chemical oxygen demand (COD) removal efficiency and methane (CH4) production rate were 89% and 2.10 L CH4/L/d, respectively, at the peak influent COD concentration (110.4 g/L) and organic loading rate (7.5 g COD/L/d). The 454 pyrosequencing results clearly indicated heterogeneous distribution of bacterial communities at different vertical locations (upper, middle, and bottom) of the UMAR. Firmicutes was the dominant (>70%) phylum at the middle and bottom parts, while Deltaproteobacteria and Chloroflexi were only found in the upper part. Potential functions of the bacteria were discussed to speculate on their roles in the anaerobic performance of the UMAR system. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 33:1226–1234, 2017
A new type of gene‐disruption cassette with a rescue gene for Pichia pastoris
Authors: Shibui Tatsuro , Hara Hiroyoshi
Published: August 2017

Pichia pastoris has been used for the production of many recombinant proteins, and many useful mutant strains have been created. However, the efficiency of mutant isolation by gene‐targeting is usually low and the procedure is difficult for those inexperienced in yeast genetics. In order to overcome these issues, we developed a new gene‐disruption system with a rescue gene using an inducible Cre/mutant–loxP system. With only short homology regions, the gene‐disruption cassette of the system replaces its target–gene locus containing a mutation with a compensatory rescue gene. As the cassette contains the AOX1 promoter‐driven Cre gene, when targeted strains are grown on media containing methanol, the DNA fragment, i.e., the marker, rescue and Cre genes, between the mutant‐loxP sequences in the cassette is excised, leaving only the remaining mutant‐loxP sequence in the genome, and consequently a target gene‐disrupted mutant can be isolated. The system was initially validated on ADE2 gene disruption, where the disruption can easily be detected by color‐change of the colonies. Then, the system was applied for knocking‐out URA3 and OCH1 genes, reported to be difficult to accomplish by conventional gene‐targeting methods. All three gene‐disruption cassettes with their rescue genes replaced their target genes, and the Cre/mutant–loxP system worked well to successfully isolate their knock‐out mutants. This study identified a new gene‐disruption system that could be used to effectively and strategically knock out genes of interest, especially whose deletion is detrimental to growth, without using special strains, e.g., deficient in nonhomologous end‐joining, in P. pastoris. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1201–1208, 2017
Effect of zinc chloride and PEG concentrations on the critical flux during tangential flow microfiltration of BSA precipitates
Authors: Li Zhao , Zydney Andrew L.
Published: August 2017

There is renewed interest in the possibility of using precipitation for initial capture of high value therapeutic proteins as part of an integrated continuous downstream process. These precipitates can be continuously washed using tangential flow filtration, with long term operation achieved by operating the membrane modules below the critical filtrate flux for fouling. Our hypothesis was that the critical flux for the precipitated protein would be a function of the properties of the precipitate as determined by the precipitation conditions. We evaluated the critical flux using a flux‐stepping procedure for model protein precipitates (bovine serum albumin) generated using a combination of a crosslinking agent (zinc chloride) and an excluded volume precipitant (polyethylene glycol [PEG]). The critical flux varied with shear rate to approximately the 1/3 power, consistent with predictions of the classical polarization model. The critical flux increased significantly with increasing zinc chloride concentration, going from 60 L/m2/h for a 2 mM ZnCl2 solution to 200 L/m2/h for an 8 mM ZnCl2 solution. In contrast, the critical flux achieved a maximum value at an intermediate PEG concentration. Independent measurements of the effective size and viscosity of the protein precipitates were used to obtain additional understanding of the effects of ZnCl2 and PEG on the precipitation and the critical flux. These results provide important insights into the development of effective tangential flow filtration systems for processing large quantities of precipitated protein as would be required for large scale continuous protein purification by precipitation. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1561–1567, 2017
Experimental design and metabolic flux analysis tools to optimize industrially relevant Haemophilus influenzae type b growth medium
Authors: da Silva Mateus Ribeiro , Andreia Freixo Portela Carla , Maria Ferreira Albani Silvia , Rizzo de Paiva Paola , Massako Tanizaki Martha , Zangirolami Teresa Cristina
Published: August 2017

Haemophilus influenzae type b (Hib), a Gram‐negative capsulated bacterium, is a causative agent of meningitis worldwide. The capsular polysaccharide, a high molecular mass polymer consisting of the repeated units of the polyribosyl‐ribitol‐phosphate, is considered the main virulence factor and it is used as an antigen to vaccines, conjugated to a carrier protein. The industrial production of the polysaccharide requires the cultivation of Hib in rich medium, which impacts process costs and product recovery. In this study, a central composite rotational experimental design strategy was used to access the influence of key components of culture medium (soy peptone, yeast extract and glucose) on biomass formation and polysaccharide production in shake‐flasks. The optimized medium formulation, containing half of the usual yeast extract and soytone concentrations, was further validated in batch bioreactor cultivations. High polysaccharide production (∼500 mg/L) was obtained in a cheaper and more competitive production process for use in Hib vaccine production. In addition, simulations of a metabolic model describing Hib central metabolism were used to assess the role of key amino acids on growth. A chemically defined medium supplemented only with amino acids from α‐ketoglutarate and oxaloacetate families as well as phenylalanine was suggested as a promising alternative for reduced acetate accumulation and enhanced polysaccharide production in Hib cultures. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1508–1519, 2017
Validating distribution models for twelve endemic bird species of tropical dry forest in western Mexico
Authors: Ortega‐Huerta Miguel A. , Vega‐Rivera Jorge H.
Published: August 2017

Considering the high biodiversity and conservation concerns of the tropical dry forest, this study aim is to predict and evaluate the potential and current distributions of twelve species of endemic birds which distribute along the western slope of Mexico. The main goal is to evaluate altogether different methods for predicting actual species distribution models (ADMs) of the twelve species including the identification of key environmental potential limiting factors.ADMs for twelve endemic Mexican birds were generated and validated by means of applying: (1) three widely used species niche modeling approaches (ENFA, Garp, and Maxent); (2) two thresholding methods, based onROCcurves and Kappa Index, for transforming continuous models to presence/absence (binary) models; (3) documented habitat–species associations for reducing species potential distribution models (PDMs); and (4) field occurrence data for validating finalADMs. BinaryPDMs' predicted areas seemed overestimated, whileADMs looked drastically reduced and fragmented because of the approach taken for eliminating those predicted areas which were documented as unsuitable habitat types for individual species. Results indicated that both thresholding methods generated similar threshold values for species modeled by each of the three species distribution modeling algorithms (SDMAs). A Wilcoxon signed‐rank test, however, showed that Kappa values were generally higher thanROCcurve for species modeled byENFAand Maxent, while for Garp models there were no significant differences. Prediction success (e.g., true presences percentage) obtained from field occurrence data revealed a range of 50%–82% among the 12 species. The three modeling approaches applied enabled to test the application of two thresholding methods for transforming continuous to binary (presence/absence) models. The use of documented habitat preferences resulted in drastic reductions and fragmentation ofPDMs. However,ADMs predictive success rate, tested using field species occurrence data, varied between 50 and 82%.
A Paper‐Based Microfluidic Fuel Cell with Hydrogen Peroxide as Fuel and Oxidant
Authors: Yan Xiaohui , Xu Ao , Zeng Lin , Gao Ping , Zhao Tianshou
Published: August 2017

The ever‐growing interest in portable electronics, especially wearable devices, imposes great demands on power sources that are compact. A paper‐based microfluidic fuel cell for portable electronics that uses H2O2 as both fuel and oxidant is reported herein. Unlike conventional microfluidic fuel cells, which rely on a colaminar flow of anolyte and catholyte, the present fuel cell is realized by the selective catalysis of H2O2, and it can eliminate concerns about fuel management and disturbance by bubbles. Silver nanowires and carbon nanotube (CNT)‐supported Prussian Blue are chosen as the anode and cathode catalyst, respectively, to catalyze the oxidation and reduction reactions. Results show that the present microfluidic fuel cell system is able to offer a peak power density as high as 0.88 mW cm−2. Additional striking features of the present fuel cell are that it does not require precious‐metal catalysts and the used fuel, H2O2, is a carbon‐free and sustainable energy carrier.
The fabrication and the use of immobilized cells as test organisms in a ferricyanide-based toxicity biosensor
Authors: Liu Chang , Xu Yingchao , Han Xiao , Chang Xiaojie
Published: August 2017

Cell immobilization is an effective method to prolong the lifetime of a microorganism and has proven feasibility in some other biosensors. Thus, we studied the use of Escherichia coli immobilized by agar, gelatin, an agar/gelatin mixture, chitosan, and polyvinyl alcohol (PVA) to screen toxicity electrochemically. The E. coli immobilized by PVA gel showed the highest apparent bioactivity and the longest storage time in pH 7.0 phosphate-buffered saline solution. Furthermore, the E. coli immobilized by different gels was applied in the toxicity determination via a reported ferricyanide-mediated electrochemical method, where 3,5-dichlorophenol (DCP) was used as a model toxin. The E. coli immobilized by PVA showed the highest sensitivity to DCP, and the corresponding value of 50% inhibition concentration was 9.62 mg L−1. Inhibition concentrations were in the range of 6.32 to 13.75% when the E. coli immobilized by PVA was challenged by wastewater, which were comparable with values obtained with the standard luminescent bacteria method (effective inhibition were in the range 7.96–25.42% for the same samples). Given the apparent bioactivity, storage ability, and sensitivity to toxin, PVA was the best polymer to confine cells among the polymers used in the present study. Environ Toxicol Chem 2018;37:329–335. © 2017 SETAC
Grounds for Refusal of Recognition of (Quasi‐) Annex Judgements in the Recast European Insolvency Regulation
Authors: Fabok Zoltan
Published: August 2017

Insolvency‐related (annex) actions and judgements fall within the scope of the Recast European Insolvency Regulation (‘Recast EIR’). That instrument both determines international jurisdiction regarding annex actions and sets up a simplified recognition system for annex judgements. However, tension between the Recast EIR's provisions on jurisdiction and recognition arises when a court of a state different from the state of insolvency erroneously assumes jurisdiction for annex actions. Such ‘quasi‐annex’ judgements rendered by foreign courts erroneously assuming jurisdiction threaten the integrity of the insolvency proceedings. Besides, the quasi‐annex judgements may violate the effectiveness and efficiency of the insolvency proceedings as well as the principle of legal certainty. In this article, it is argued that even the current legal framework may offer some ways to avoid the recognition of such quasi‐annex judgements. First, the scope of the public policy exception may be extended in order to protect the integrity of the insolvency proceedings from the quasi‐annex judgements rendered by foreign courts erroneously assuming jurisdiction. Second, it may be argued that quasi‐annex judgements do not equal real annex judgements and therefore do not enjoy the automatic recognition system provided by the Recast EIR. At the same time, their close connection to the insolvency proceedings – disregarded by the forum erroneously assuming jurisdiction – may exclude quasi‐annex judgements from the scope of the Brussels Ibis Regulation, as well. As a consequence, those quasi‐annex judgements may fall within the gap between the two regulations, meaning that no European instrument instructs the courts of the member state addressed to recognise quasi‐annex judgements. Copyright © 2017 INSOL International and John Wiley & Sons, Ltd.
Real‐time respiratory phase matching between 2D fluoroscopic images and 3D CT images for precise percutaneous lung biopsy
Authors: Weon Chijun , Kim Mina , Park Chang Min , Ra Jong Beom
Published: August 2017

Purpose

A 3D CT image is used along with real‐time 2D fluoroscopic images in the state‐of‐the‐art cone‐beam CT system to guide percutaneous lung biopsy (PLB). To improve the guiding accuracy by compensating for respiratory motion, we propose an algorithm for real‐time matching of 2D fluoroscopic images to multiple 3D CT images of different respiratory phases that is robust to the small movement and deformation due to cardiac motion.

Methods

Based on the transformations obtained from nonrigid registration between two 3D CT images acquired at expiratory and inspiratory phases, we first generate sequential 3D CT images (or a 4D CT image) and the corresponding 2D digitally reconstructed radiographs (DRRs) of vessels. We then determine 3D CT images corresponding to each real‐time 2D fluoroscopic image, by matching the 2D fluoroscopic image to a 2D DRR.

Results

Quantitative evaluations performed with 20 clinical datasets show that registration errors of anatomical features between a 2D fluoroscopic image and its matched 2D DRR are less than 3 mm on average. Registration errors of a target lesion are determined to be roughly 3 mm on average for 10 datasets.

Conclusions

We propose a real‐time matching algorithm to compensate for respiratory motion between a 2D fluoroscopic image and 3D CT images of the lung, regardless of cardiac motion, based on a newly improved matching measure. The proposed algorithm can improve the accuracy of a guiding system for the PLB by providing 3D images precisely registered to 2D fluoroscopic images in real‐time, without time‐consuming respiratory‐gated or cardiac‐gated CT images.
Direct plasma stimuli including electrostimulation and OH radical induce transient increase in intracellular Ca2+ and uptake of a middle‐size membrane‐impermeable molecule
Authors: Sasaki Shota , Hokari Yutaro , Kumada Akiko , Kanzaki Makoto , Kaneko Toshiro
Published: August 2017

Despite the promising potential of medical treatments based on non‐equilibrium atmospheric‐pressure plasma, most of the underlying mechanisms remain unknown. Here we report that direct plasma irradiation (DPI) can induce transient increase in intracellular calcium (Ca2+) concentrations, thereby playing key roles in many cellular processes as well as the uptake of middle‐size membrane‐impermeable molecules, which did not occur with indirect plasma irradiation (IPI). Experimental measurements using a Pockels voltage probe and gelling chemical reagent showed that electric field of 150 kV/cm and hydroxyl radical (OH) supply to cell cultures were induced by DPI under a typical condition compared with IPI. In addition, significant inhibition of the OH scavenger D‐mannitol indicated involvement of OH in those DPI‐induced cellular responses. These results facilitate the elucidation of plasma‐cell interaction and the development of plasma devices for medical treatments.
Competing risk analysis in a large cardiovascular clinical trial: An APEX substudy
Authors: Arbetter Douglas F. , Jain Purva , Yee Megan K. , Michalak Nathan , Hernandez Adrian F. , Hull Russell D. , Goldhaber Samuel Z. , Harrington Robert A. , Gold Alex , Cohen Alexander T. , Gibson C. Michael
Published: August 2017

Competing risk methods are time‐to‐event analyses that account for fatal and/or nonfatal events that may potentially alter or prevent a subject from experiencing the primary endpoint. Competing risk methods may provide a more accurate and less biased estimate of the incidence of an outcome but are rarely applied in cardiology trials. APEX investigated the efficacy of extended‐duration betrixaban versus standard‐duration enoxaparin to prevent a composite of symptomatic deep‐vein thrombosis (proximal or distal), nonfatal pulmonary embolism, or venous thromboembolism (VTE)–related death in acute medically ill patients (n = 7513). The aim of the current analysis was to determine the efficacy of betrixaban vs standard‐duration enoxaparin accounting for non‐VTE–related deaths using the Fine and Gray method for competing risks. The proportion of non‐VTE–related death was similar in both the betrixaban (133, 3.6%) and enoxaparin (136, 3.7%) arms, P = .85. Both the traditional Kaplan‐Meier method and the Fine and Gray method accounting for non‐VTE–related death as a competing risk showed equal reduction of VTE events when comparing betrixaban to enoxaparin (HR/SHR = 0.65, 95% 0.42‐0.99, P = 0.046). Due to the similar proportion of non‐VTE–related deaths in both treatment arms and the use of a univariate model, the Fine and Gray method provided identical results to the traditional Cox model. Using the Fine and Gray method in addition to the traditional Cox proportional hazards method can indicate whether the presence of a competing risk, which is dependent of the outcome, altered the risk estimate.
Purity analysis for JavaScript through abstract interpretation
Authors: Nicolay Jens , Stiévenart Quentin , De Meuter Wolfgang , De Roover Coen
Published: August 2017

We present a static analysis for determining whether and to what extent functions in JavaScript programs are pure. To this end, the analysis classifies functions as pure functions, observers, or procedures. A function is pure if none of its executions generate or depend upon externally observable side effects. A function is an observer as soon as one of its executions depends on an external side effect, but none of its executions generate observable side effects. Otherwise, the function is classified as a procedure. Function executions and associated callers are found by traversing all reachable function execution contexts on the call stack at the point where an effect occurs. Our approach is based on a flow analysis that, in addition to computing traditional control and value flow, keeps track of read and write effects. To increase the precision of our purity analysis, we combine it with an intraprocedural analysis that determines freshness of variables and objects. We formalize the core aspects of our technique and discuss its implementation and results on common JavaScript benchmarks. Results show that our approach is capable of determining function purity in the presence of higher‐order functions, dynamic property expressions, and prototypal inheritance. When compared with existing purity analyses, we find that our approach is as precise or more precise than the existing analyses.
Regional and Midlife Crises
Authors: Baron Beth
Published: August 2017

I wanted to talk to you today about regional and midlife crises. It is not my midlife crisis—I'll save that for another time though I'm happy to hear about yours—but rather MESA's at fifty that I would like to discuss.
A LATTER-DAY MYSTERY: THOMAS CARLYLE AND EUGÈNE SUE
Authors: Jordan Alexander Hugh
Published: August 2017

The names Thomas Carlyle(1795–1881) and Eugène Sue (1804–1857) rarely figure in the same sentence. Carlyle is commonly remembered as a dour Scots Calvinist and eminent Victorian; Sue, in contrast, as a sensational French novelist, and sybarite-turned-champagne-socialist. Nevertheless, the following article will contend that Carlyle was in fact familiar with the works of Sue, to such an extent that he adapted passages from the latter'sMystères de Paris(1842–1843) in his ownLatter-Day Pamphlets(1850). First, the article will offer a brief sketch of Sue and his novel, before discussing their reception amongst Carlyle's circle of friends and acquaintances. It will then suggest that Carlyle himself was likely to have read the novel, and then proceed to compare the relevant passages of theMystèresand thePamphlets, which together constitute the primary focus of the article. Finally, it will be argued that this matter is far from being a mere curiosity, of concern only to the most obsessive of Carlyle scholars. To the contrary, it will be suggested that in understanding what Carlyle did with Sue, we will be better able to grasp the meaning of some of the more notorious passages of his most notorious work, and particularly their political thrust. In doing so, the article will build upon a number of recent studies of the reception of French literature in Victorian Britain, and will also reopen the question of Carlyle's debts to French socialism, an issue that continues to be a matter of some controversy amongst Carlyle scholars.
Switching roles: a qualitative study of staff experiences of being dialectical behaviour therapists within the National Health Service in England
Authors: Hutton Rebecca , Hodge Suzanne , Tighe Martin
Published: August 2017

Many National Health Service (NHS) Trusts in England have invested in dialectical behavioural therapy (DBT) for mental health service users. The experiences of NHS staff delivering DBT were explored using semi-structured interviews with six dialectical behaviour therapists working in secondary mental health services within the NHS. The aim was to consider the impact on staff of adding the DBT therapist role onto their existing job role. Interview data were analysed using thematic analysis. Six themes were inductively generated from the data: DBT as a useful framework; DBT as the most satisfying part of the job; ‘Worzel Gummidge heads’– conflicts in roles; ‘DBT buddies’– the importance of informal support; uncertainty about the future; and recursivity – using DBT skills personally. Interactions between themes, implications for the service and future research directions are discussed. Key findings suggest that the addition of the DBT therapist role, as well as the recursive nature of DBT, has a positive impact professionally and personally. However, the service context within which participants were working can lead this additional role to cause increased demands and therefore stress, reducing that positive impact.
Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters
Authors: Wu Linwei , Yang Yunfeng , Chen Si , Jason Shi Zhou , Zhao Mengxin , Zhu Zhenwei , Yang Sihang , Qu Yuanyuan , Ma Qiao , He Zhili , Zhou Jizhong , He Qiang
Published: August 2017

The ecological concept of the r-K life history strategy is widely applied in macro-ecology to characterize functional traits of taxa. However, its adoption in microbial communities is limited, owing to the lack of a measureable, convenient functional trait for classification. In this study, we performed an experiment of stepwise organic amendments in triplicate anaerobic digesters. We found that high resource availability significantly favored microbial r-strategists such as Bacillus spp. Incremental resource availability heightened average rRNA operon copy number of microbial community, resulting in a strong, positive correlation (r>0.74, P<0.008). This study quantifies how resource availability manipulations influence microbial community composition and supports the idea that rRNA operon copy number is an ecologically meaningful trait which reflects resource availability.
Stability of gene expression in human T cells in different gravity environments is clustered in chromosomal region 11p15.4
Authors: Thiel Cora S. , Huge Andreas , Hauschild Swantje , Tauber Svantje , Lauber Beatrice A. , Polzer Jennifer , Paulsen Katrin , Lier Hartwin , Engelmann Frank , Schmitz Burkhard , Schütte Andreas , Layer Liliana E. , Ullrich Oliver
Published: August 2017

In the last decades, a plethora of in vitro studies with living human cells contributed a vast amount of knowledge about cellular and molecular effects of microgravity. Previous studies focused mostly on the identification of gravity-responsive genes, whereas a multi-platform analysis at an integrative level, which specifically evaluates the extent and robustness of transcriptional response to an altered gravity environment was not performed so far. Therefore, we investigated the stability of gene expression response in non-activated human Jurkat T lymphocytic cells in different gravity environments through the combination of parabolic flights with a suborbital ballistic rocket and 2D clinostat and centrifuge experiments, using strict controls for excluding all possible other factors of influence. We revealed an overall high stability of gene expression in microgravity and identified olfactory gene expression in the chromosomal region 11p15.4 as particularly robust to altered gravity. We identified that classical reference genesABCA5,GAPDH,HPRT1,PLA2G4A, andRPL13Awere stably expressed in all tested gravity conditions and platforms, whileABCA5andGAPDHwere also known to be stably expressed in U937 cells in all gravity conditions. In summary, 10–20% of all transcripts remained totally unchanged in any gravitational environment tested (between 10−4and 9 g), 20–40% remained unchanged in microgravity (between 10−4and 10−2 g) and 97–99% were not significantly altered in microgravity if strict exclusion criteria were applied. Therefore, we suppose a high stability of gene expression in microgravity. Comparison with other stressors suggests that microgravity alters gene expression homeostasis not stronger than other environmental factors.
Reduced age-associated brain changes in expert meditators: a multimodal neuroimaging pilot study
Authors: Chételat Gaël , Mézenge Florence , Tomadesso Clémence , Landeau Brigitte , Arenaza-Urquijo Eider , Rauchs Géraldine , André Claire , de Flores Robin , Egret Stéphanie , Gonneaud Julie , Poisnel Géraldine , Chocat Anne , Quillard Anne , Desgranges Béatrice , Bloch Jean-Gérard , Ricard Matthieu , Lutz Antoine
Published: August 2017

Aging is associated with progressive cerebral volume and glucose metabolism decreases. Conditions such as stress and sleep difficulties exacerbate these changes and are risk factors for Alzheimer’s disease. Meditation practice, aiming towards stress reduction and emotion regulation, can downregulate these adverse factors. In this pilot study, we explored the possibility that lifelong meditation practice might reduce age-related brain changes by comparing structural MRI and FDG-PET data in 6 elderly expert meditators versus 67 elderly controls. We found increased gray matter volume and/or FDG metabolism in elderly expert meditators compared to controls in the bilateral ventromedial prefrontal and anterior cingulate cortex, insula, temporo-parietal junction, and posterior cingulate cortex /precuneus. Most of these regions were also those exhibiting the strongest effects of age when assessed in a cohort of 186 controls aged 20 to 87 years. Moreover, complementary analyses showed that these changes were still observed when adjusting for lifestyle factors or using a smaller group of controls matched for education. Pending replication in a larger cohort of elderly expert meditators and longitudinal studies, these findings suggest that meditation practice could reduce age-associated structural and functional brain changes.
Indirect genetic effects: a key component of the genetic architecture of behaviour
Authors: Santostefano Francesca , Wilson Alastair J. , Niemelä Petri T. , Dingemanse Niels J.
Published: August 2017

Behavioural ecology research increasingly focuses on why genetic behavioural variation can persist despite selection. Evolutionary theory predicts that directional selection leads to evolutionary change while depleting standing genetic variation. Nevertheless, evolutionary stasis may occur for traits involved in social interactions. This requires tight negative genetic correlations between direct genetic effects (DGEs) of an individual’s genes on its own phenotype and the indirect genetic effects (IGEs) it has on conspecifics, as this could diminish the amount of genetic variation available to selection to act upon. We tested this prediction using a pedigreed laboratory population of Mediterranean field crickets (Gryllus bimaculatus), in which both exploratory tendency and aggression are heritable. We found that genotypes predisposed to be aggressive (due to DGEs) strongly decreased aggressiveness in opponents (due to IGEs). As a consequence, the variance in total breeding values was reduced to almost zero, implying that IGEs indeed greatly contribute to the occurrence of evolutionary stasis. IGEs were further associated with genetic variation in a non-social behaviour: explorative genotypes elicited most aggression in opponents. These key findings imply that IGEs indeed represent an important overlooked mechanism that can impact evolutionary dynamics of traits under selection.
Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation
Authors: Impey Soren , Jopson Timothy , Pelz Carl , Tafessu Amanuel , Fareh Fatema , Zuloaga Damian , Marzulla Tessa , Riparip Lara-Kirstie , Stewart Blair , Rosi Susanna , Turker Mitchell S. , Raber Jacob
Published: August 2017

The brain’s response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways. Significant overlap was observed between DNA methylation changes at the 2 and 20-week time points demonstrating specificity and retention of changes in response to radiation. Moreover, a novel class of DNA methylation change was observed following an environmental challenge (i.e. space irradiation), characterized by both increased and decreased 5hmC levels along the entire gene body. These changes were mapped to genes encoding neuronal functions including postsynaptic gene ontology categories. Thus, the brain’s response to proton irradiation is both specific and prolonged and involves novel remodeling of non-random regions of the epigenome.
Stable multi-GeV electron accelerator driven by waveform-controlled PW laser pulses
Authors: Kim Hyung Taek , Pathak V. B. , Hong Pae Ki , Lifschitz A. , Sylla F. , Shin Jung Hun , Hojbota C. , Lee Seong Ku , Sung Jae Hee , Lee Hwang Woon , Guillaume E. , Thaury C. , Nakajima Kazuhisa , Vieira J. , Silva L. O. , Malka V. , Nam Chang Hee
Published: August 2017

The achievable energy and the stability of accelerated electron beams have been the most critical issues in laser wakefield acceleration. As laser propagation, plasma wave formation and electron acceleration are highly nonlinear processes, the laser wakefield acceleration (LWFA) is extremely sensitive to initial experimental conditions. We propose a simple and elegant waveform control method for the LWFA process to enhance the performance of a laser electron accelerator by applying a fully optical and programmable technique to control the chirp of PW laser pulses. We found sensitive dependence of energy and stability of electron beams on the spectral phase of laser pulses and obtained stable 2-GeV electron beams from a 1-cm gas cell of helium. The waveform control technique for LWFA would prompt practical applications of centimeter-scale GeV-electron accelerators to a compact radiation sources in the x-ray and γ-ray regions.
Wfs1- deficient rats develop primary symptoms of Wolfram syndrome: insulin-dependent diabetes, optic nerve atrophy and medullary degeneration
Authors: Plaas Mario , Seppa Kadri , Reimets Riin , Jagomäe Toomas , Toots Maarja , Koppel Tuuliki , Vallisoo Tuuli , Nigul Mait , Heinla Indrek , Meier Riho , Kaasik Allen , Piirsoo Andres , Hickey Miriam A. , Terasmaa Anton , Vasar Eero
Published: August 2017

Wolfram syndrome (WS) is a rare autosomal-recessive disorder that is caused by mutations in the WFS1 gene and is characterized by juvenile-onset diabetes, optic atrophy, hearing loss and a number of other complications. Here, we describe the creation and phenotype of Wfs1 mutant rats, in which exon 5 of the Wfs1 gene is deleted, resulting in a loss of 27 amino acids from the WFS1 protein sequence. These Wfs1-ex5-KO232 rats show progressive glucose intolerance, which culminates in the development of diabetes mellitus, glycosuria, hyperglycaemia and severe body weight loss by 12 months of age. Beta cell mass is reduced in older mutant rats, which is accompanied by decreased glucose-stimulated insulin secretion from 3 months of age. Medullary volume is decreased in older Wfs1-ex5-KO232 rats, with the largest decreases at the level of the inferior olive. Finally, older Wfs1-ex5-KO232 rats show retinal gliosis and optic nerve atrophy at 15 months of age. Electron microscopy revealed axonal degeneration and disorganization of the myelin in the optic nerves of older Wfs1-ex5-KO232 rats. The phenotype of Wfs1-ex5-KO232 rats indicates that they have the core symptoms of WS. Therefore, we present a novel rat model of WS.