bluuebunny/crossref_metadata_2025 huggingface dataset:
MapSets: Visualizing Embedded and Clustered Graphs
Authors: Efrat Alon , Hu Yifan , Kobourov Stephen , Pupyrev Sergey
Published: August 2015

In addition to objects and relationships between them, groups or clusters of objects are an essential part of many real-world datasets: party affiliation in political networks, types of living organisms in the tree of life, movie genres in the internet movie database. In recent visualization methods, such group information is conveyed by explicit regions that enclose related elements. However, when in addition to fixed cluster membership, the input elements also have fixed positions in space (e.g., geo-referenced data), it becomes difficult to produce readable visualizations. In such fixed-clustering and fixed-embedding settings, some methods produce fragmented regions, while other produce contiguous (connected) regions that may contain overlaps even if the input clusters are disjoint. Both fragmented regions and unnecessary overlaps have a detrimental effect on the interpretation of the drawing. With this in mind, we propose MapSets: a visualization technique that combines the advantages of both methods, producing maps with non-fragmented and non-overlapping regions. The proposed method relies on a theoretically sound geometric algorithm which guarantees contiguity and disjointness of the regions, and also optimizes the convexity of the regions. A fully functional implementation is available in an online system and is used in a comparison with related earlier methods.
Cdc6 ATPase activity disengages Cdc6 from the pre-replicative complex to promote DNA replication
Authors: Chang FuJung , Riera Alberto , Evrin Cecile , Sun Jingchuan , Li Huilin , Speck Christian , Weinreich Michael
Published: August 2015

To initiate DNA replication, cells first load an MCM helicase double hexamer at origins in a reaction requiring ORC, Cdc6, and Cdt1, also called pre-replicative complex (pre-RC) assembly. The essential mechanistic role of Cdc6 ATP hydrolysis in this reaction is still incompletely understood. Here, we show that although Cdc6 ATP hydrolysis is essential to initiate DNA replication, it is not essential for MCM loading. Using purified proteins, an ATPase-defective Cdc6 mutant ‘Cdc6-E224Q’ promoted MCM loading on DNA. Cdc6-E224Q also promoted MCM binding at origins in vivo but cells remained blocked in G1-phase. If after loading MCM, Cdc6-E224Q was degraded, cells entered an apparently normal S-phase and replicated DNA, a phenotype seen with two additional Cdc6 ATPase-defective mutants. Cdc6 ATP hydrolysis is therefore required for Cdc6 disengagement from the pre-RC after helicase loading to advance subsequent steps in helicase activation in vivo.
Genome-wide errant targeting by Hairy
Authors: Kok Kurtulus , Ay Ahmet , Li Li M , Arnosti David N
Published: August 2015

Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
Neuropilin-2/Semaphorin-3F-mediated repulsion promotes inner hair cell innervation by spiral ganglion neurons
Authors: Coate Thomas M , Spita Nathalie A , Zhang Kaidi D , Isgrig Kevin T , Kelley Matthew W
Published: August 2015

Auditory function is dependent on the formation of specific innervation patterns between mechanosensory hair cells (HCs) and afferent spiral ganglion neurons (SGNs). In particular, type I SGNs must precisely connect with inner HCs (IHCs) while avoiding connections with nearby outer HCs (OHCs). The factors that mediate these patterning events are largely unknown. Using sparse-labeling and time-lapse imaging, we visualized for the first time the behaviors of developing SGNs including active retraction of processes from OHCs, suggesting that some type I SGNs contact OHCs before forming synapses with IHCs. In addition, we demonstrate that expression of Semaphorin-3F in the OHC region inhibits type I SGN process extension by activating Neuropilin-2 receptors expressed on SGNs. These results suggest a model in which cochlear innervation patterns by type I SGNs are determined, at least in part, through a Semaphorin-3F-mediated inhibitory signal that impedes processes from extending beyond the IHC region.
Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network
Authors: Axelrod Kevin , Sanchez Alvaro , Gore Jeff
Published: August 2015

Microorganisms often exhibit a history-dependent phenotypic response after exposure to a stimulus which can be imperative for proper function. However, cells frequently experience unexpected environmental perturbations that might induce phenotypic switching. How cells maintain phenotypic states in the face of environmental fluctuations remains an open question. Here, we use environmental perturbations to characterize the resilience of phenotypic states in a synthetic gene network near a critical transition. We find that far from the critical transition an environmental perturbation may induce little to no phenotypic switching, whereas close to the critical transition the same perturbation can cause many cells to switch phenotypic states. This loss of resilience was observed for perturbations that interact directly with the gene circuit as well as for a variety of generic perturbations-such as salt, ethanol, or temperature shocks-that alter the state of the cell more broadly. We obtain qualitatively similar findings in natural gene circuits, such as the yeast GAL network. Our findings illustrate how phenotypic memory can become destabilized by environmental variability near a critical transition.
Small molecule inhibition of Csk alters affinity recognition by T cells
Authors: Manz Boryana N , Tan Ying Xim , Courtney Adam H , Rutaganira Florentine , Palmer Ed , Shokat Kevan M , Weiss Arthur
Published: August 2015

The C-terminal Src kinase (Csk), the primary negative regulator of Src-family kinases (SFK), plays a crucial role in controlling basal and inducible receptor signaling. To investigate how Csk activity regulates T cell antigen receptor (TCR) signaling, we utilized a mouse expressing mutated Csk (CskAS) whose catalytic activity is specifically and rapidly inhibited by a small molecule. Inhibition of CskAS during TCR stimulation led to stronger and more prolonged TCR signaling and to increased proliferation. Inhibition of CskAS enhanced activation by weak but strictly cognate agonists. Titration of Csk inhibition revealed that a very small increase in SFK activity was sufficient to potentiate T cell responses to weak agonists. Csk plays an important role, not only in basal signaling, but also in setting the TCR signaling threshold and affinity recognition.
The 133-kDa N-terminal domain enables myosin 15 to maintain mechanotransducing stereocilia and is essential for hearing
Authors: Fang Qing , Indzhykulian Artur A , Mustapha Mirna , Riordan Gavin P , Dolan David F , Friedman Thomas B , Belyantseva Inna A , Frolenkov Gregory I , Camper Sally A , Bird Jonathan E
Published: August 2015

The precise assembly of inner ear hair cell stereocilia into rows of increasing height is critical for mechanotransduction and the sense of hearing. Yet, how the lengths of actin-based stereocilia are regulated remains poorly understood. Mutations of the molecular motor myosin 15 stunt stereocilia growth and cause deafness. We found that hair cells express two isoforms of myosin 15 that differ by inclusion of an 133-kDa N-terminal domain, and that these isoforms can selectively traffic to different stereocilia rows. Using an isoform-specific knockout mouse, we show that hair cells expressing only the small isoform remarkably develop normal stereocilia bundles. However, a critical subset of stereocilia with active mechanotransducer channels subsequently retracts. The larger isoform with the 133-kDa N-terminal domain traffics to these specialized stereocilia and prevents disassembly of their actin core. Our results show that myosin 15 isoforms can navigate between functionally distinct classes of stereocilia, and are independently required to assemble and then maintain the intricate hair bundle architecture.
Evidence for the episodic erosion of the Medusae Fossae Formation preserved within the youngest volcanic province on Mars
Authors: Morgan Gareth A. , Campbell Bruce A. , Carter Lynn M. , Plaut Jeffrey J.
Published: August 2015

We use orbital SHAllow RADar (SHARAD) sounder data to three‐dimensionally visualize the subsurface structure of Elysium Planitia, the youngest volcanic province on Mars. Our results reveal an emplacement history consisting of multiple groups of overlapping lava flow units, originating from different sources. The uniquely complex “radar stratigraphy” of Elysium Planitia, relative to other volcanic regions, requires a distinct mechanism to generate the numerous reflectors observed in SHARAD data. Sedimentary deposits interbedded with successive batches of lava flows could account for the elaborate pattern of reflectors. We infer that widespread, rapidly emplaced material sourced from the enigmatic Medusae Fossae Formation (MFF) creates these sedimentary layers. This implies that episodes of atmospheric activity, perhaps linked with the obliquity of Mars, periodically erode and redeposit material from the MFF across a large region.
Ion temperature anisotropy across a magnetotail reconnection jet
Authors: Hietala H. , Drake J. F. , Phan T. D. , Eastwood J. P. , McFadden J. P.
Published: August 2015

A significant fraction of the energy released by magnetotail reconnection appears to go into ion heating, but this heating is generally anisotropic. We examine ARTEMIS dual‐spacecraft observations of a long‐duration magnetotail exhaust generated by antiparallel reconnection in conjunction with particle‐in‐cell simulations, showing spatial variations in the anisotropy across the outflow far (>100di) downstream of the X line. A consistent pattern is found in both the spacecraft data and the simulations: While the total temperature across the exhaust is rather constant, near the boundaries Ti,|| dominates. The plasma is well above the firehose threshold within patchy spatial regions at |BX|∈[0.1,0.5]B0, suggesting that the drive for the instability is strong and the instability is too weak to relax the anisotropy. At the midplane (
), Ti,⊥>Ti,|| and ions undergo Speiser‐like motion despite the large distance from the X line.
Resolute Bay Incoherent Scatter Radar observations of plasma structures in the vicinity of polar holes
Authors: Makarevich Roman A. , Lamarche L. J. , Nicolls M. J.
Published: August 2015

The Resolute Bay Incoherent Scatter Radar North (RISR‐N) data collected between January 2012 and June 2013 are employed to identify and analyze 14 events with significant plasma density depressions (Ne<4 × 1010 m−3) in the winter polar cap ionosphere. The RISR‐N observations near a magnetic latitude (MLAT) of 85°N refer to the region poleward of the previously identified polar hole‐auroral cavity region 70°–80° MLAT where extremely low densities (down to 2 × 108 m−3 near 300 km in altitude) are found at times. Multipoint observations by RISR‐N are also characterized by multiple series of propagating local density enhancements (plasma structures) both well outside and in the vicinity of polar holes. A superposed epoch analysis of plasma density and convection reveals that the density depressions tend to reach their minimum near the reversal of the meridional convection component. The wavelet analysis of plasma density time series shows that the wave power is enhanced within the depressions and tends to peak near the density minimum. The plasma structures are more elongated at mesoscales (>150 km), with no apparent differences between structure shapes outside and inside low‐density regions. The structure propagation velocity is perpendicular to its elongation direction and consistent with that of the large‐scale plasma convection. The observations indicate that large‐scale density depressions can form under a variety of convection conditions and that plasma structuring processes outside the depressions may be responsible for their partial filling.
Observations of storm time midlatitude ion‐neutral coupling using SuperDARN radars and NATION Fabry‐Perot interferometers
Authors: Joshi P. P. , H. Baker J. B. , Ruohoniemi J. M. , Makela J. J. , Fisher D. J. , Harding B. J. , Frissell N. A. , Thomas E. G.
Published: August 2015

Ion drag is known to play an important role in driving neutral thermosphere circulation at auroral latitudes, especially during the main phase of geomagnetic storms. During the recovery phase, the neutrals are known to drive the ions and generate ionospheric electric fields and currents via the disturbance dynamo mechanism. At midlatitudes, the precise interplay between ions and neutrals is less understood largely because of the paucity of measurements that have been available. In this work, we investigate ion‐neutral coupling at middle latitudes using colocated ion drift velocity measurements obtained from Super Dual Auroral Radar Network radars and neutral wind velocity and temperature measurements obtained from the North American Thermosphere Ionosphere Observing Network (NATION) Fabry‐Perot interferometers. We examine one recent storm period on 2–3 October 2013 during both the main phase and late recovery phase. By using ion‐neutral momentum exchange theory and a time‐lagged correlation analysis, we analyze the coupling time scales and dominant driving mechanisms. We observe that during the main phase the neutrals respond to the ion convection on a time scale of ∼84 min which is significantly faster than what would be expected from local ion drag momentum forcing alone. This suggests that other storm time influences are important for driving the neutrals during the main phase, such as Joule heating. During the late recovery phase, the neutrals are observed to drive the ion convection without any significant time delay, consistent with the so‐called “neutral fly wheel effect” or disturbance dynamo persisting well into the late recovery phase.
Synconvergence flow inside and at the margin of orogenic plateaus: Lithospheric‐scale experimental approach
Authors: Bajolet Flora , Chardon Dominique , Martinod Joseph , Gapais Denis , Kermarrec Jean‐Jacques
Published: August 2015

This study investigates three‐dimensional flow modes of orogenic plateaus by means of physical modeling. Experiments consist of shortening two contiguous lithospheres of contrasting strength, one being a weak plateau‐type lithosphere and the other a strong craton‐type lithosphere. The lateral boundaries are either totally confined or allow escape toward a lateral foreland on one side. Two synconvergence flow regimes are distinguished, which are governed by the balance between the gravity potential and the strength of the plateau crust and the resistance of its lateral foreland. The first regime implies transversal (orogen‐normal) injection of plateau lower crust into the collision zone as a result of confinement of the plateau by an increasingly stiffer lateral boundary. As a precursor mechanism to channel flow, transversal injection responds to downward thickening of the plateau crust that is forcedly extruded into the orogenic wedge. The second regime is that of collapse‐driven lateral escape of the plateau. This regime is established after a threshold is attained in the interplate coupling in the collision zone, which allows the gravity potential of the plateau to overcome the resistance of its lateral boundary. Under the collapse‐driven escape regime (orogen parallel), such as that governing Tibet during the last 13 Ma, most of the convergence in the plateau and the top and rear of the collisional wedge is transformed into lateral flow and extension.
Tidal resonance in icy satellites with subsurface oceans
Authors: Kamata Shunichi , Matsuyama Isamu , Nimmo Francis
Published: August 2015

Tidal dissipation is a major heat source for the icy satellites of the giant planets. Several icy satellites likely possess a subsurface ocean underneath an ice shell. Previous studies of tidal dissipation on icy satellites, however, have either assumed a static ocean or ignored the effect of the ice lid on subsurface ocean dynamics. In this study, we examine inertial effects on tidal deformation of satellites with a dynamic ocean overlain by an ice lid based on viscoelasto‐gravitational theory. Although ocean dynamics is treated in a simplified fashion, we find a resonant configuration when the phase velocity of ocean gravity waves is similar to that of the tidal bulge. This condition is achieved when a subsurface ocean is thin (<1 km). The enhanced deformation (increased h2 and k2 Love numbers) near the resonant configuration would lead to enhanced tidal heating in the solid lid. A static ocean formulation gives an accurate result only if the ocean thickness is much larger than the resonant thickness. The resonant configuration strongly depends on the properties of the shell, demonstrating the importance of the presence of a shell on tidal dissipation.
Dry deposition of polycyclic aromatic compounds to various land covers in the Athabasca oil sands region
Authors: Zhang Leiming , Cheng Irene , Wu Zhiyong , Harner Tom , Schuster Jasmin , Charland Jean‐Pierre , Muir Derek , Parnis J. Mark
Published: August 2015

A framework was developed to estimate dry deposition of polycyclic aromatic compounds (PACs), including 17 polycyclic aromatic hydrocarbons (PAHs), 21 alkylated PAHs, and 5 parent and alkylated dibenzothiophenes (DBTs), to various land covers surrounding three monitoring sites in the Athabasca oil sands region. Modeled dry deposition velocities for various gaseous PACs and over various land covers were mostly in the range of 0.01–0.5 cm s−1 with median and annual mean values between 0.08 and 0.24 cm s−1, comparable with literature values obtained from field studies. Annual dry deposition of the sum of PAHs was estimated to range from 330 to 560 μg m−2 over forested canopies surrounding the three sites and from 270 to 490 μg m−2 over grass and shrubs. The corresponding values are 3920–5380 and 2850–4920 μg m−2 for the sum of 21 alkylated PAHs, and are 230–1120 and 450–930 μg m−2 for the sum of 5 DBTs. The three monitoring sites are situated nearby the Athabasca River, and the direct annual atmospheric dry deposition to water surface was estimated to range from 350 to 500, 3170 to 4530, and 170 to 840 μg m−2 for PAHs, alkylated PAHs, and DBTs, respectively. Alkylated PAHs contributed 80% of the total dry and 60% of the total wet deposition budget, suggesting the importance of including this group of PAHs in the atmospheric deposition budget estimation for subsequent ecosystem impact studies.
Popularity differentially predicts reactive and proactive aggression in early adolescence
Authors: Stoltz Sabine , Cillessen Antonius H.N. , van den Berg Yvonne H.M. , Gommans Rob
Published: August 2015

Previous research has indicated that peer popularity is associated with aggressive behavior. However, it is not yet clear whether popularity is uniquely related to different functions of aggression. In this study, we examined associations between peer‐perceived popularity, and reactive and proactive aggression using a cross‐sectional and a longitudinal design. Yearly sociometric measures of popularity, and reactive and proactive aggression were gathered from 266 seventh and eight grade adolescents (Mage grade 7 = 12.80, SDage = .40). Popularity was positively correlated with proactive aggression and negatively correlated with reactive aggression, both concurrently as over time. Curvilinear trends indicated that a significant minority of low versus high popular adolescents showed both functions of aggression. Somewhat stronger effects of popularity on proactive aggression were found for boys than girls. Stably popular adolescents showed the highest levels of proactive aggression, whereas stably unpopular youth showed the highest levels of reactive aggression. Implications and directions for future research are discussed. Aggr. Behav. 42:29–40, 2016. © 2015 Wiley Periodicals, Inc.
Antiquity and geographic distribution of cranial modification among the prehistoric groups of Fuego‐Patagonia, Chile
Authors: Alfonso‐Durrruty Marta P. , Giles Bretton T. , Misarti Nicole , San Roman Manuel , Morello Flavia
Published: August 2015

Objectives

Nineteenth and twentieth century documents testify that four ethnic groups, generally classified as terrestrial hunters or canoe nomads, inhabited Fuego‐Patagonia. Archaeologically, however, their presence and temporal depth remains unknown. This study analyzes the antiquity and geographic distribution of cranial modification, a highly visible symbol of social identity, in Fuego‐Patagonia, Chile, to assess whether it expressed ethnic affiliation.

Materials and Methods

A total of 60 adult skulls from Southern Patagonia (n = 32; 53.3%) and Tierra del Fuego (n = 28; 46.7%) were examined for age‐at‐death, sex and cranial modification with standard methods. Individuals were further categorized as terrestrial (n = 26; 43.3%), marine (n = 21; 35%) or indetermined hunter‐gatherers (n = 13; 21.7%) based on the archaeological site's characteristics, geographic location, and isotopic information.

Results

Thirty percent (n = 18) of the skulls in this study were modified, and most of the modified skulls (n = 15) presented a tabular‐erect shape. No statistically significant differences were identified between Fuegians and Patagonians, males or females, or between the different types of adaptation and geographic locations.

Discussion

Thus, this Late Holocene, widely distributed practice, was not a reflection of ethnicity, but a material expression of information circulation and the complex social relations that these small‐size groups had with one another. These results suggest that the emergence of modern ethnic identities in the region is a historic process that resulted from the interaction of local groups with European and Criollos. Am J Phys Anthropol 158:607–623, 2015. © 2015 Wiley Periodicals, Inc.
Information entropy as a measure of tunneling and quantum confinement in a symmetric double‐well potential
Authors: Mukherjee Neetik , Roy Arunesh , Roy Amlan K.
Published: August 2015

Information entropic measures such as Fisher information, Shannon entropy, Onicescu energy and Onicescu Shannon entropy of a symmetric double‐well potential are calculated in both position and momentum space. Eigenvalues and eigenvectors of this system are obtained through a variation‐induced exact diagonalization procedure. The information entropy‐based uncertainty relation is shown to be a better measure than conventional uncertainty product in interpreting purely quantum mechanical phenomena, such as, tunneling and quantum confinement in this case. Additionally, the phase‐space description provides a semi‐classical explanation for this feature. Total information entropy and phase‐space area show similar behavior with increasing barrier height.

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Thiophene π‐bridge effect on photovoltaic performances of dithienosilole and bithiazole backboned polymers
Authors: Zheng Huilin , Gu Chuantao , Zhu Qianqian , Bao Xichang , Wen Shuguang , Qiu Meng , Zhu Dangqiang , Sun Mingliang , Yang Renqiang
Published: August 2015

In this article, two dithienosilole (DTS) and bithiazole (BTz) backboned donor–acceptor (D‐A) copolymers with (poly{5‐(5‐(4,4‐bis(2‐ethylhexyl)‐4H‐silolo[3,2‐b:4,5‐b']dithiophen‐2‐yl)thiophen‐2‐yl)‐4,4'‐dinonyl‐5'‐(thiophen‐2‐yl)‐2,2'‐bithiazole} (PDTS‐DTBTz)) and without (poly{5‐(4,4‐bis(2‐ethylhexyl)‐4H‐silolo[3,2‐b:4,5‐b']dithiophen‐2‐yl)‐4,4'‐dinonyl‐2,2'‐bithiazole} (PDTS‐BTz)) thiophene π‐bridge were synthesized to study the influence of thiophene π‐bridge on their photovoltaic performances. Both polymers show similar band gap, but polymer with thiophene π‐bridge (PDTS‐DTBTz) has a higher molecular weight, narrower polydispersity index (PDI), more planar geometry, higher crystallinity, higher hole mobility, and better miscibility with fullerene (polymer solar cells (PSCs) acceptor). Although PDTS‐BTz polymer based PSCs devices show higher open circuit voltage (Voc), PDTS‐DTBTz polymer does show higher power conversion efficiency (PCE) with improved short circuit current density (Jsc) and fill factor (FF). The present results indicate that thiophene π‐bridge does contribute to the PSCs performances of dithienosilole and bithiazole backboned copolymer. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42798.
Calcium ion‐mediated grafting of a phosphate‐containing monomer
Authors: Suzuki Shuko , Wentrup‐Byrne Edeline , Chandler‐Temple Adrienne , Shah Nevil , Grøndahl Lisbeth
Published: August 2015

Grafting of monoacryloxyethyl phosphate onto expanded polytetrafluoroethylene was achieved using simultaneous grafting with the aim of improving the membrane wettability and mineralization capacity. This study explored the effect of adding calcium ions to the grafting solution and observed increased graft yield and wettability when compared with samples grafted in the absence of calcium ions. Fourier transform infrared spectroscopy mapping found the graft copolymer to be distributed in a patchy manner across the surface as well as throughout the membrane. Through X‐ray photoelectron spectroscopy analysis, it was found that calcium ions were incorporated into the graft copolymer and could be extracted using a basic ethylenediaminetetraacetic acid solution without reduction in graft yield. This implies that the presence of calcium ions is affecting the graft yield by increasing the local concentration of monomer near the surface during the grafting process. Investigation of the mineralization capacity of the grafted membranes in simulated body fluid revealed that the increased wettability of the membranes rather than the presence of the calcium ions affected the mineralization outcome. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42808.
Clarification technologies for monoclonal antibody manufacturing processes: Current state and future perspectives
Authors: Singh Nripen , Arunkumar Abhiram , Chollangi Srinivas , Tan Zhijun George , Borys Michael , Li Zheng Jian
Published: August 2015

Considerable progress has been made increasing productivity of cell cultures to meet the rapidly growing demand for antibody biopharmaceuticals through increased cell densities and longer culture times. This in turn has dramatically increased the burden of process and product related impurities on the purification processes. In addition, current trends in the biopharmaceutical industry point toward both increased productivity and targeting smaller patient populations for new indications. Taken together, these developments are driving the industry to explore alternative separation technologies as a future manufacturing strategy. Clarification technologies well established in other industries, such as flocculation and precipitation are increasingly considered as a viable solution to address this bottleneck in antibody processes. However, several technical issues need to be fully addressed including suitability as a platform application, robustness, process cost, toxicity, and clearance. This review will focus on recent efforts to incorporate new generation clarification technologies for mammalian cell cultures producing monoclonal antibodies as well as challenges to their implementation supported by a case study. Biotechnol. Bioeng. 2016;113: 698–716. © 2015 Wiley Periodicals, Inc.
Development of a bench‐top device for parallel climate‐controlled recordings of neuronal cultures activity with microelectrode arrays
Authors: Regalia Giulia , Biffi Emilia , Achilli Silvia , Ferrigno Giancarlo , Menegon Andrea , Pedrocchi Alessandra
Published: August 2015

Two binding requirements for in vitro studies on long‐term neuronal networks dynamics are (i) finely controlled environmental conditions to keep neuronal cultures viable and provide reliable data for more than a few hours and (ii) parallel operation on multiple neuronal cultures to shorten experimental time scales and enhance data reproducibility. In order to fulfill these needs with a Microelectrode Arrays (MEA)‐based system, we designed a stand‐alone device that permits to uninterruptedly monitor neuronal cultures activity over long periods, overcoming drawbacks of existing MEA platforms. We integrated in a single device: (i) a closed chamber housing four MEAs equipped with access for chemical manipulations, (ii) environmental control systems and embedded sensors to reproduce and remotely monitor the standard in vitro culture environment on the lab bench (i.e. in terms of temperature, air CO2 and relative humidity), and (iii) a modular MEA interface analog front‐end for reliable and parallel recordings. The system has been proven to assure environmental conditions stable, physiological and homogeneos across different cultures. Prolonged recordings (up to 10 days) of spontaneous and pharmacologically stimulated neuronal culture activity have not shown signs of rundown thanks to the environmental stability and have not required to withdraw the cells from the chamber for culture medium manipulations. This system represents an effective MEA‐based solution to elucidate neuronal network phenomena with slow dynamics, such as long‐term plasticity, effects of chronic pharmacological stimulations or late‐onset pathological mechanisms. Biotechnol. Bioeng. 2016;113: 403–413. © 2015 Wiley Periodicals, Inc.
Performance benchmarking of four cell‐free protein expression systems
Authors: Gagoski Dejan , Polinkovsky Mark E. , Mureev Sergey , Kunert Anne , Johnston Wayne , Gambin Yann , Alexandrov Kirill
Published: August 2015

Over the last half century, a range of cell‐free protein expression systems based on pro‐ and eukaryotic organisms have been developed and have found a range of applications, from structural biology to directed protein evolution. While it is generally accepted that significant differences in performance among systems exist, there is a paucity of systematic experimental studies supporting this notion. Here, we took advantage of the species‐independent translation initiation sequence to express and characterize 87 N‐terminally GFP‐tagged human cytosolic proteins of different sizes in E. coli, wheat germ (WGE), HeLa, and Leishmania‐based (LTE) cell‐free systems. Using a combination of single‐molecule fluorescence spectroscopy, SDS‐PAGE, and Western blot analysis, we assessed the expression yields, the fraction of full‐length translation product, and aggregation propensity for each of these systems. Our results demonstrate that the E. coli system has the highest expression yields. However, we observe that high expression levels are accompanied by production of truncated species—particularly pronounced in the case of proteins larger than 70 kDa. Furthermore, proteins produced in the E. coli system display high aggregation propensity, with only 10% of tested proteins being produced in predominantly monodispersed form. The WGE system was the most productive among eukaryotic systems tested. Finally, HeLa and LTE show comparable protein yields that are considerably lower than the ones achieved in the E. coli and WGE systems. The protein products produced in the HeLa system display slightly higher integrity, whereas the LTE‐produced proteins have the lowest aggregation propensity among the systems analyzed. The high quality of HeLa‐ and LTE‐produced proteins enable their analysis without purification and make them suitable for analysis of multi‐domain eukaryotic proteins. Biotechnol. Bioeng. 2016;113: 292–300. © 2015 Wiley Periodicals, Inc.
Towards the industrialization of new biosurfactants: Biotechnological opportunities for the lactone esterase gene from Starmerella bombicola
Authors: Roelants Sophie L.K.W. , Ciesielska Katarzyna , De Maeseneire Sofie L. , Moens Helena , Everaert Bernd , Verweire Stijn , Denon Quenten , Vanlerberghe Brecht , Van Bogaert Inge N.A. , Van der Meeren Paul , Devreese Bart , Soetaert Wim
Published: August 2015

Although sophorolipids (SLs) produced by S. bombicola are a real showcase for the industrialization of microbial biosurfactants, some important drawbacks are associated with this efficient biological process, e.g., the simultaneous production of acidic and lactonic SLs. Depending on the application, there is a requirement for the naturally produced mixture to be manipulated to give defined ratios of the components. Recently, the enzyme responsible for the lactonization of SLs was discovered. The discovery of the gene encoding this lactone esterase (sble) enabled the development of promising S. bombicola strains producing either solely lactonic (using a sble overexpression strain described in this paper: oe sble) or solely acidic SLs (using a sble deletion strain, which was recently described, but not characterized yet: Δsble). The new S. bombicola strains were used to investigate the production processes (fermentation and purification) of either lactonic or acidic SLs. The strains maintain the high inherent productivities of the wild‐type or even perform slightly better and thus represent a realistic industrial opportunity. 100% acidic SLs with a mixed acetylation pattern were obtained for the Δsble strain, while the inherent capacity to selectively produce lactonic SLs was significantly increased (+42%) for the oe sble strain (99% lactonic SLs). Moreover, the regulatory effect of citrate on lactone SL formation for the wild‐type was absent in this new strain, which indicates that it is more robust and better suited for the industrial production of lactonic SLs. Basic parameters were determined for the purified SLs, which confirm that the two new strains produce molecules with distinctive properties of which the application potential can now easily be investigated independently. Biotechnol. Bioeng. 2016;113: 550–559. © 2015 Wiley Periodicals, Inc.
Physiological effects of pH gradients on Escherichia coli during plasmid DNA production
Authors: Cortés José T. , Flores Noemí , Bolívar Francisco , Lara Alvaro R. , Ramírez Octavio T.
Published: August 2015

A two‐compartment scale‐down system was used to mimic pH heterogeneities that can occur in large‐scale bioreactors. The system consisted of two interconnected stirred tank reactors (STRs) where one of them represented the conditions of the bulk of the fluid and the second one the zone of alkali addition for pH control. The working volumes ratio of the STRs was set to 20:1 in order to simulate the relative sizes of the bulk and alkali addition zones, respectively, in large‐scale bioreactors. Residence times (tR) in the alkali addition STR of 60, 120, 180, and 240 s were simulated during batch cultures of an engineered Escherichia coli strain that produced plasmid DNA (pDNA). pH gradients of up to 0.9 units, between the two compartments, were attained. The kinetic, stoichiometric, and pDNA topological changes due to the pH gradients were studied and compared to cultures at constant pH of 7.2 and 8.0. As the tR increased, the pDNA and biomass yields, as well as pDNA final titer decreased, whereas the accumulation of organic acids increased. Furthermore, the transcriptional response of 10 selected genes to alkaline stress (pH 8.0) and pH gradients was monitored at different stages of the cultures. The selected genes coded for ion transporters, amino acids catabolism enzymes, and transcriptional regulators. The transcriptional response of genes coding for amino acids catabolism, in terms of relative transcription level and stage of maximal expression, was different when the alkaline stress was constant or transient. This suggests the activation of different mechanisms by E. coli to cope with pH fluctuations compared to constant alkaline pH. Moreover, the transcriptional response of genes related to negative control of DNA synthesis did not correlate with the lower pDNA yields. This is the first study that reports the effects of pH gradients on pDNA production by E. coli cultures. The information presented can be useful for the design of better bioreactor scale‐up strategies. Biotechnol. Bioeng. 2016;113: 598–611. © 2015 Wiley Periodicals, Inc.
Isolation and Biosynthesis of an Azoxyalkene Compound Produced by a Multiple Gene Disruptant of Streptomyces rochei
Authors: Kunitake Hirofumi , Hiramatsu Takahiro , Kinashi Haruyasu , Arakawa Kenji
Published: August 2015

Streptomyces rochei 7434AN4 predominantly produces lankacidin and lankamycin under normal culture conditions, thus suggesting that other biosynthetic gene clusters for secondary metabolites are silent. To identify the silent metabolites of 7434AN4, we constructed mutant KA57 with multiple disruptions of the transcriptional repressor srrB and the biosynthesis genes for both antibiotics. KA57 accumulated a compound (KA57A) with a strong UV absorption at 235 nm, not detected in the parent strain or other mutants. Various spectroscopic analyses revealed that KA57A is an azoxyalkene compound with the molecular formula C10H20N2O3 and with the R configuration at C‐2. Biosynthesis of KA57A was also studied by feeding with labeled acetates, amino acids, and 1‐hexylamine. The hexenyl moiety (C1′–C6′) was derived from fatty acid, whereas the 3‐aminobutan‐1,2‐diol moiety (C1–C4) was derived from C‐2 of acetate (C1) and serine (C2–C4). Incorporation of [1,1‐2H2]‐1‐hexylamine indicated that C1′–C2′ dehydrogenation occurs as the final step of biosynthesis.
Tuning the Surface Chemistry of Nanoporous Carbons for Enhanced Nanoconfined Photochemical Activity
Authors: Velasco Leticia F. , Gomis‐Berenguer Alicia , Lima Joao C. , Ania Conchi O.
Published: August 2015

We showed the effect of surface oxidation on the conversion of light into a chemical reaction in the confined pore space of nanoporous carbons. The photoactivity of carbons is caused by the combination of high porosity and the presence of photoreactive sites that favor the splitting of the exciton inside the pores, which boosts its efficient use in chemical reactions. The incorporation of O‐containing groups in the carbon matrix decreased the photoconversion inside the pores, although values were higher than those attained in solution. This is attributed to the lower stabilization of the exciton through the delocalization within the conjugated sp2 network of the basal planes because of the electron‐withdrawing effect of the O‐containing groups. The photochemical conversion of light inside the pores is very sensitive to the acidic/basic nature of the O‐containing groups of the carbon matrix, and can be enhanced by balancing the surface composition, porosity, and electronic mobility.
Chirality Sensing With Stereodynamic Biphenolate Zinc Complexes
Authors: Bentley Keith W. , de los Santos Zeus A. , Weiss Mary J. , Wolf Christian
Published: August 2015

Two bidentate ligands consisting of a fluxional polyarylacetylene framework with terminal phenol groups were synthesized. Reaction with diethylzinc gives stereodynamic complexes that undergo distinct asymmetric transformation of the first kind upon binding of chiral amines and amino alcohols. The substrate‐to‐ligand chirality imprinting at the zinc coordination sphere results in characteristic circular dichroism signals that can be used for direct enantiomeric excess (ee) analysis. This chemosensing approach bears potential for high‐throughput ee screening with small sample amounts and reduced solvent waste compared to traditional high‐performance liquid chromatography methods. Chirality 27:700–707, 2015. © 2015 Wiley Periodicals, Inc.
Overview of palliative care and hospice services
Authors: Wordingham Sara E. , Swetz Keith M.
Published: August 2015

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Pyogenic liver abscess
Authors: Longworth Sarah , Han Jennifer
Published: August 2015

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Amebic liver abscess
Authors: Anesi Judith A. , Gluckman Stephen
Published: August 2015

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Hepatitis C treatment: Back to the warehouse
Authors: Rice John P.
Published: August 2015

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Design and simulation of a multilayer Halbach magnet for NMR
Authors: Chen Qiaoyan , Zhang Guangcai , Xu Yajie , Yang Xiaodong
Published: August 2015

Halbach magnet is a type of permanent magnet generating a relatively high and homogeneous magnetic field. It is suitable for Nuclear Magnetic Resonance (NMR) studies of small volume chemical or biological samples. In this article, the model of a Halbach magnet made from an odd number of cylindrical layers is proposed for the first time. Then after the optimization of interlayer distances for odd layers Halbach cylinders, the model is verified by the simulation with a magnet inner radius of 30 mm and an outer radius of 49 mm. Moreover, the disturbance of uniformity in 5 mm DSV (Diameter of Spherical Volume) is presented with errors in magnetic strength and angular variation. As a result, a minimum uniformity of 46 ppm inside a 5 mm DSV is achieved, while it increases practically in the presence of magnetic blocks errors. The good performance of the Halbach magnet with odd layers may find potential applications in NMR. © 2015 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 45B: 134–141, 2015
Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile
Authors: Castañeda Luis E. , Godoy Karina , Manzano Marlene , Marquet Pablo A. , Barbosa Olga
Published: August 2015

Natural ecosystems provide services to agriculture such as pest control, soil nutrients, and key microbial components. These services and others in turn provide essential elements that fuel biomass productivity. Responsible agricultural management and conservation of natural habitats can enhance these ecosystem services. Vineyards are currently driving land‐use changes in many Mediterranean ecosystems. These land‐use changes could have important effects on the supporting ecosystems services related to the soil properties and the microbial communities associated with forests and vineyard soils. Here, we explore soil bacterial and fungal communities present in sclerophyllous forests and organic vineyards from three different wine growing areas in central Chile. We employed terminal restriction fragment length polymorphisms (T‐RFLP) to describe the soil microbial communities inhabiting native forests and vineyards in central Chile. We found that the bacterial community changed between the sampled growing areas; however, the fungal community did not differ. At the local scale, our findings show that fungal communities differed between habitats because fungi species might be more sensitive to land‐use change compared to bacterial species, as bacterial communities did not change between forests and vineyards. We discuss these findings based on the sensitivity of microbial communities to soil properties and land‐use change. Finally, we focus our conclusions on the importance of naturally derived ecosystem services to vineyards.
Transcription factor co‐occupied regions in the murine genome constitute T‐helper‐cell subtype‐specific enhancers
Authors: Fang Zhuo , Hecklau Katharina , Gross Fridolin , Bachmann Ivo , Venzke Melanie , Karl Martin , Schuchhardt Johannes , Radbruch Andreas , Herzel Hanspeter , Baumgrass Ria
Published: August 2015

Transcription factors (TFs) regulate cell‐type‐specific gene expression programs by combinatorial binding to cis‐genomic elements, particularly enhancers, subsequently leading to the recruitment of cofactors, and the general transcriptional machinery to target genes. Using data integration of genome‐wide TF binding profiles, we defined regions with combinatorial binding of lineage‐specific master TFs (T‐BET, GATA3, and ROR‐γt) and STATs (STAT1 and STAT4, STAT6, and STAT3) in murine T helper (Th) 1, Th2, and Th17 cells, respectively. Stringently excluding promoter regions, we revealed precise genomic elements which were preferentially associated with the enhancer marks p300 and H3K4me1. Furthermore, closely adjacent TF co‐occupied regions constituted larger enhancer domains in the respective Th‐cell subset (177 in Th1, 141 in Th2, and 266 in Th17 cells) with characteristics of so‐called super‐enhancers. Importantly, 89% of these super‐enhancer regions were Th‐cell subtype‐specific. Genes associated with super‐enhancers, including relevant Th‐cell genes (such as Ifng in Th1, Il13 in Th2, and Il17a in Th17 cells), showed strong transcriptional activity. Altogether, the discovered catalog of enhancers provides information about crucial Th‐cell subtype‐specific regulatory hubs, which will be useful for revealing cell‐type‐specific gene regulation processes.
Environmental life cycle assessments of emerging anode materials for Li‐ion batteries‐metal oxide NPs
Authors: Padashbarmchi Zahra , Hamidian Amir Hossein , Khorasani Nematolah , Kazemzad Mahmood , McCabe Annie , Halog Anthony
Published: August 2015

Lithium ion batteries are widely used to meet ever‐growing energy demands. They are also considered as energy storage devices to decrease the concerns about limited energy sources and associated environmental issues by displacing a large fraction of gasoline use in HEV and PHEV. Due to these concerns, intensive research on alternative energy conversion and storage systems with high efficiency, low cost, and environmental benignity has been stimulated worldwide. Recently, nanostructured 3d‐metal oxides MOx (M = Cu, Fe, Co, etc.) have been widely studied as anode materials for lithium‐ion batteries (LIBs) owing to their high energy capacity. Electrodes synthesized by Fe, Co, or Cu have more lithium‐ion storage capacity (over 600 mAh/g) compared to the commercial electrodes synthesized by graphite (about 372 mAh/g). The life cycle assessment (LCA) methodology is utilized in order to identify environmental hotspots and aid in directing design towards regenerative and environmentally sustainable product design and process development. The main aim of this study is to investigate environmental effects of different lithium‐ion batteries with different metal oxides as anode active material. The life cycle assessment results showed that metal oxides like Iron oxide can be a promising anode material due to their much higher energy density. In the production phase, the most important stage is production of NMP (N‐methyl‐2‐pyrrolidone, an organic solvent in electrode preparation), for batteries with graphite and anode active material production for batteries with copper oxides. © 2015 American Institute of Chemical Engineers Environ Prog, 34: 1740–1747, 2015