bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of the diffusion-layer thickness during electrodeposition on the synthesis of nano core/shell Sn–O–C composite as an anode of lithium secondary batteries
Authors: Jeong Moongook , Yokoshima Tokihiko , Nara Hiroki , Momma Toshiyuki , Osaka Tetsuya
Published: May 2014

Electrodeposition of nano core/shell Sn–O–C composite anodes for lithium secondary batteries and improvement of cycle performances by a simple agitation technique.
Protic ionic liquid [TMG][Ac] as an efficient, homogeneous and recyclable catalyst for one-pot four-component synthesis of 2H-indazolo[2,1-b]phthalazine-triones and dihydro-1H-pyrano[2,3-c]pyrazol-6-ones
Authors: Veisi Hojat , Manesh Abbas Amini , Khankhani Narges , Ghorbani-Vaghei Ramin
Published: May 2014

A mildly basic ionic liquid was found to be a very effective basic catalyst at 80 °C.
Plasma enhanced atomic layer deposition of Fe2O3 thin films
Authors: Ramachandran Ranjith K. , Dendooven Jolien , Detavernier Christophe
Published: May 2014

We demonstrate an ALD process for Fe2O3 that relies upon sequential pulsing of ter-Butyl ferrocene (TBF) and O2 plasma and enables the deposition from temperatures as low as 150 °C.
Water dispersible Ag@polyaniline-pectin as supercapacitor electrode for physiological environment
Authors: Amarnath Chellachamy A. , Venkatesan Nandakumar , Doble Mukesh , Sawant Shilpa N.
Published: May 2014

We report the synthesis of a water dispersible Ag@PANI-PEC nanocomposite which exhibits electroactivity, biocompatibility, antibacterial properties and the ability to work as a supercapacitor electrode in a physiological environment.
Acoustic and Perceptual Effects of Left–Right Laryngeal Asymmetries Based on Computational Modeling
Authors: Samlan Robin A. , Story Brad H. , Lotto Andrew J. , Bunton Kate
Published: May 2014

Purpose

Computational modeling was used to examine the consequences of 5 different laryngeal asymmetries on acoustic and perceptual measures of vocal function.

Method

A kinematic vocal fold model was used to impose 5 laryngeal asymmetries: adduction, edge bulging, nodal point ratio, amplitude of vibration, and starting phase. Thirty /a/ and /ɪ/ vowels were generated for each asymmetry and analyzed acoustically using cepstral peak prominence (CPP), harmonics-to-noise ratio (HNR), and 3 measures of spectral slope (H1*-H2*, B0-B1, and B0-B2). Twenty listeners rated voice quality for a subset of the productions.

Results

Increasingly asymmetric adduction, bulging, and nodal point ratio explained significant variance in perceptual rating (
R
2
= .05,
p
< .001). The same factors resulted in generally decreasing CPP, HNR, and B0-B2 and in increasing B0-B1. Of the acoustic measures, only CPP explained significant variance in perceived quality (
R
2
= .14,
p
< .001). Increasingly asymmetric amplitude of vibration or starting phase minimally altered vocal function or voice quality.

Conclusion

Asymmetries of adduction, bulging, and nodal point ratio drove acoustic measures and perception in the current study, whereas asymmetric amplitude of vibration and starting phase demonstrated minimal influence on the acoustic signal or voice quality.

Supplemental Material

https://doi.org/10.23641/asha.6170459
Finite‐time H∞ control with average dwell‐time constraint for time‐delay Markov jump systems governed by deterministic switches
Authors: Luan Xiaoli , Zhao Changzhong , Liu Fei
Published: May 2014

This study considers the problem of finite‐time H∞ control for a class of discrete‐time time‐delay Markov jump linear systems governed by deterministic switches. By allowing the stochastic Lyapunov function to increase at every switching instant with a limited increase rate, new results on the stochastic finite‐time boundness with given H∞ disturbance attenuation level are derived. Moreover, the coupling relationship among time‐delay, average dwell time and given finite‐time horizon of the underlying system is obtained through an average dwell‐time constraint. Finally, one example is given to demonstrate the validity of the obtained results.
Multifractal properties of ball milling dynamics
Authors: Budroni M. A. , Pilosu V. , Delogu F. , Rustici M.
Published: May 2014

This work focuses on the dynamics of a ball inside the reactor of a ball mill. We show that the distribution of collisions at the reactor walls exhibits multifractal properties in a wide region of the parameter space defining the geometrical characteristics of the reactor and the collision elasticity. This feature points to the presence of restricted self-organized zones of the reactor walls where the ball preferentially collides and the mechanical energy is mainly dissipated.
The impact of argon admixture on the c-axis oriented growth of direct current magnetron sputtered ScxAl1−xN thin films
Authors: Mayrhofer P. M. , Eisenmenger-Sittner C. , Stöger-Pollach M. , Euchner H. , Bittner A. , Schmid U.
Published: May 2014

The piezoelectric properties of wurtzite aluminium nitride (w-AlN) are enhanced by alloying with scandium (Sc), thus offering superior properties for applications in micro electro-mechanical systems devices. ScxAl1−xN thin films have been prepared by DC reactive magnetron sputtering on Si (100) substrates from a single target. When targeting a concentration range from x = 0 up to x = 0.15, the preparation conditions have been optimized by varying the Ar/N2 ratio in the sputtering gas. To incorporate an increasing Sc concentration, a higher Ar/N2 ratio has to be applied during the deposition process. Hence, the argon concentration in the sputtering gas becomes a crucial parameter for microstructure-related parameters. To determine phase purity, degree of c-axis orientation, lattice parameter, and grain size, the ScxAl1−xN thin films were investigated by techniques, such as scanning electron microscopy, transmission electron microscopy, and X-ray diffraction.
Europium-doped aluminum oxide phosphors as indicators for frontal polymerization dynamics
Authors: Carranza Arturo , Gewin Mariah , Pojman John A.
Published: May 2014

In this study, we present an inexpensive and practical method that allows the monitoring and visualization of front polymerization, propagation, and dynamics. Commercially available europium-doped aluminum oxide powders were combined with video imaging to visualize free-radical propagating polymer fronts. In order to demonstrate the applicability of this method, frontal copolymerization reactions of propoxylated glycerin triacrylate (EB53), pentaerythritol triacrylate (PETA), and pentaerythritol tetra-acrylate (PETEA) with 1,1-Bis(tert-butylperoxy)-3,3,5-trimethylcyclohexane (Luperox 231®) as an initiator were studied and compared to the results obtained by IR imaging. Systems exhibiting higher filler loading, higher EB53 content, and less acrylated monomers showed a marked decrease in front velocity, while those with more acrylated monomers and higher crosslinking density showed a marked increase in front velocity. Finally, in order to show the potential of the imaging technique, we studied fronts propagating in planar and spherical geometries.
Identification of interactions in fractional-order systems with high dimensions
Authors: Ji Xiaoxi , Wu Yu , Sheng Wenbo , Lin Wei
Published: May 2014

This article proposes an approach to identify fractional-order systems with sparse interaction structures and high dimensions when observation data are supposed to be experimentally available. This approach includes two steps: first, it is to estimate the value of the fractional order by taking into account the solution properties of fractional-order systems; second, it is to identify the interaction coefficients among the system variables by employing the compressed sensing technique. An error analysis is provided analytically for this approach and a further improved approach is also proposed. Moreover, the applicability of the proposed approach is fully illustrated by two examples: one is to estimate the mutual interactions in a complex dynamical network described by fractional-order systems, and the other is to identify a high fractional-order and homogeneous sequential differential equation, which is frequently used to describe viscoelastic phenomena. All the results demonstrate the feasibility of figuring out the system mechanisms behind the data experimentally observed in physical or biological systems with viscoelastic evolution characters.
Paper-based colorimetric enzyme linked immunosorbent assay fabricated by laser induced forward transfer
Authors: Katis Ioannis N. , Holloway Judith A. , Madsen Jens , Faust Saul N. , Garbis Spiros D. , Smith Peter J. S. , Voegeli David , Bader Dan L. , Eason Robert W. , Sones Collin L.
Published: May 2014

We report the Laser Induced Forward Transfer (LIFT) of antibodies from a liquid donor film onto paper receivers for application as point-of-care diagnostic sensors. To minimise the loss of functionality of the active biomolecules during transfer, a dynamic release layer was employed to shield the biomaterial from direct exposure to the pulsed laser source. Cellulose paper was chosen as the ideal receiver because of its inherent bio-compatibility, liquid transport properties, wide availability and low cost, all of which make it an efficient and suitable platform for point-of-care diagnostic sensors. Both enzyme-tagged and untagged IgG antibodies were LIFT-printed and their functionality was confirmed via a colorimetric enzyme-linked immunosorbent assay. Localisation of the printed antibodies was exhibited, which can allow the creation of complex 2-d patterns such as QR codes or letters for use in a final working device. Finally, a calibration curve was determined that related the intensity of the colour obtained to the concentration of active antibodies to enable quantitative assessment of the device performance. The motivation for this work was to implement a laser-based procedure for manufacturing low-cost, point-of-care diagnostic devices on paper.
Welfare of recently weaned piglets transported on unpaved roads: the effect of age and the use of straw bedding
Authors: Roldan-Santiago P. , Mota-Rojas D. , Orozco-Gregorio H. , Borderas-Tordesillas F. , Martínez-Rodríguez R. , Mora-Medina P. , Flores-Peinado S. , Sánchez-Hernández M. , Trujillo-Ortega M. E.
Published: May 2014

This study evaluated the physiological responses of piglets weaned at three different ages and transported immediately over unpaved roads with and without the use of straw bedding in the transport vehicle. The study included 270 hybrid piglets born of York–Landrace dams and Pietrain sires. The piglets were weaned and then transported at 8 days old (n = 90), 15 days old (n = 90) or 22 days old (n = 90). The duration of each trip, from the time the transport vehicle left the original site until its arrival at the destination (site 2) on the same farm, was 1 h. The piglets in each one of the three groups were divided into two subgroups: (1) transported over unpaved roads with straw bedding; (2) transported over unpaved roads without straw bedding. Three repetitions were performed for each experimental condition. To assess physiological responses to the stress caused by transport, blood samples were taken as soon as the piglets arrived at site 2. The blood variables evaluated were: pH, haematocrit (%), glucose (mg/dL), electrolytes (Na+, K+ and Ca2+) (mmol/L), lactate levels (mg/dL), partial pressures of carbon dioxide (pCO2) and oxygen (pO2) (mm Hg), bicarbonate (HCO3–), and total carbon dioxide (TCO2C). Piglets that were weaned at 8 and 15 days of age and then transported without straw bedding were found to be more susceptible to metabolic, acid–base, hydric, and gas exchange imbalances (P < 0.05). Blood concentrations of pO2, Na+, K+, Ca2+ and pH were not affected by transport in piglets weaned at 22 days of age in vehicles using straw bedding. Hence, we conclude that regardless of age and trip conditions, the transport of recently weaned piglets constitutes a stressful situation, because just 1 h of transport time was sufficient to cause imbalances in their physiological blood indicators.
Effect of different concentrations of trehalose and glycerol on the freezability of ram semen using soybean lecithin-based diluents
Authors: Bohlool Zh. , Mohammadi M. , Mehr M. Roostaei-Ali , Hossein-Zadeh N. Ghavi
Published: May 2014

This study was conducted to determine the effect of different levels of trehalose and glycerol on ram sperm cryosurvival using lecithin-based diluents. Ejaculates were collected from four rams, pooled after initial evaluation, diluted with Tris-soybean lecithin extender and split into nine equal parts. A total of 0 (T0), 50 (T50) or 100 (T100) mM of trehalose and 3% (G3), 5% (G5) or 7% (G7) of glycerol were added to each part. Sperm motility, viability, plasma membrane integrity and acrosome integrity were evaluated immediately after thawing (0 h), and subsequently after 3 h and 6 h post-thawing incubation at 37°C. Results indicated that there was interaction between trehalose and glycerol on sperm motility. In addition, interaction of trehalose and glycerol with incubation time on sperm motility, viability, plasma membrane integrity and acrosome integrity was not significant (P > 0.05). Sperm motility was greatest in the sperm treated with 100 mM trehalose and 7% glycerol (27%; P < 0.05). The effect of trehalose was significant on viability and plasma membrane integrity of ram spermatozoa (P < 0.05). The main effect of trehalose showed that sperm viability was higher in T100 (47.06%) than T50 (53.96%; P < 0.05). The highest membrane integrity was observed in T100 (47.04%; P < 0.05). Membrane integrity was higher (P < 0.05) in G5 (49.97%) than G3 (41.56%) and there was no difference between G7 (46.86%) and G3 (41.56%; P > 0.05). The best sperm viability and plasma membrane integrity was observed at 0 h (65.75% and 51.58%, respectively). It was concluded that simultaneous use of 7% glycerol and 100 mM trehalose had a desirable effect on motility of ram frozen–thawed sperm.
Possible involvement of myo-inositol in the physiological response of broilers to high doses of microbial phytase
Authors: Cowieson A. J. , Aureli R. , Guggenbuhl P. , Fru-Nji F.
Published: May 2014

The effect of high (1000–3000 phytase units (FYT)/kg) doses of microbial phytase on performance, nutrient digestibility and plasma inositol concentrations in young Ross broiler chicks was investigated in two separate experiments. In both experiments pelleted corn/soy-based diets were used and experimental duration was from Days 8 to 21 and Days 15 to 28 in Experiments 1 and 2, respectively. Treatments in Experiment 1 were arranged as a 2 × 4 + 1 factorial with two concentrations of calcium and available phosphorus and four concentrations of phytase (0, 1000, 2000 or 3000 FYT/kg), with a reference diet containing additional phosphorus and calcium from inorganic sources. In Experiment 2 only four dietary treatments were used, being a nutritionally adequate positive control, a negative control formulated to be insufficient in calcium and available phosphorus and the negative control supplemented with either 1000 or 2000 FYT/kg exogenous phytase. In both experiments, phytase improved performance relative to the appropriate control diet and increased the retention of calcium and phosphorus (P < 0.001). Tibia strength and ash content were increased (P < 0.001) by phytase addition. Plasma inositol concentrations were substantially increased (P < 0.001) by phytase addition to the diet. As inositol has been found to be an insulin mimetic in a range of animal species, these results suggest that part of the beneficial effect of high doses of phytase in broiler production may be conferred via insulin-like mechanisms. The effect of phytase on the expression of insulin-sensitive glucose transport systems, gluconeogenesis and nitrogen cycling is an area for future research. It can be concluded that phytase is effective in improving performance of broiler chicks fed diets that are sufficient and insufficient in calcium and phosphorus. Furthermore, phytase addition results in increased plasma inositol concentrations that may be beneficial in nutrient transport and protein deposition.
Consensus and stratification in the affective meaning of human sociality
Authors: Ambrasat Jens , von Scheve Christian , Conrad Markus , Schauenburg Gesche , Schröder Tobias
Published: May 2014

Significance

Humans use affective meanings of concepts as a source of information to automatically align social perceptions and behaviors with prevailing norms. Cohesive societies therefore require broad agreement on such meanings. Past research has yielded paradoxical findings. On the one hand, meanings of social concepts vary within societies, as evidenced by different lifestyles, values, and ideologies. On the other hand, studies have revealed considerable intracultural consensus and stability in affective meanings. However, such studies have been based on small and selective samples, seriously limiting our knowledge on the relative importance of consensus versus social stratification. Our large-scale study in German society fills this void, thus enhancing our understanding of the affective basis of social integration versus disintegration.
Moving Fe
2+
from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates
Authors: Behera Rabindra K. , Theil Elizabeth C.
Published: May 2014

Significance

How ions move between ion channel exits and final destinations is poorly understood. Fe
2+
substrate enters ferritin protein nanocages through cage-penetrating ion channels analogous to membrane ion channels. Fe
2+
then moves to ferritin cage enzyme (F
ox
) sites, reacting with oxygen substrate to produce diferric oxy complexes, the precursors of ferritin minerals (Fe
2
O
3
⋅H
2
O). Ferritin iron is used in heme and iron–sulfur cofactors. Monitoring rapid (ms) diferric peroxo formation in WT ferritin and E57 and E136 variants showed that these conserved residues are required for enzyme activity. Combining the results with older structural studies identifies ferritin E57 and E136 links in the Fe
2+
bucket brigade connecting ferritin ion channels and destinations. By analogy, key carboxylates in ion transporters link ion channels to cytoplasmic destinations.
Relating the metatranscriptome and metagenome of the human gut
Authors: Franzosa Eric A. , Morgan Xochitl C. , Segata Nicola , Waldron Levi , Reyes Joshua , Earl Ashlee M. , Giannoukos Georgia , Boylan Matthew R. , Ciulla Dawn , Gevers Dirk , Izard Jacques , Garrett Wendy S. , Chan Andrew T. , Huttenhower Curtis
Published: May 2014

Significance

Recent years have seen incredible growth in both the scale and specificity of projects analyzing the microbial organisms living in and on the human body (the human microbiome). Such studies typically require subjects to report to clinics for sample collection, a complicated practice that is impractical for large studies. To address these issues, we developed a protocol that allows subjects to collect microbiome samples at home and ship them to laboratories for multiple different types of molecular analysis. Measurements of microbial species, gene, and gene transcript composition within self-collected samples were consistent across sampling methods. In addition, our subsequent analysis of these samples revealed interesting similarities and differences between the measured functional potential and functional activity of the human microbiome.
Mycobacterium tuberculosis
FtsX extracellular domain activates the peptidoglycan hydrolase, RipC
Authors: Mavrici Daniela , Marakalala Mohlopheni J. , Holton James M. , Prigozhin Daniil M. , Gee Christine L. , Zhang Yanjia J. , Rubin Eric J. , Alber Tom
Published: May 2014

Significance

During growth and division, bacterial cells partition the cell wall to daughter cells, but the “inside-out” signals that regulate peptidoglycan (PG) hydrolysis are not well understood. Our studies of mycobacterial proteins achieve in vitro reconstitution of the regulation of the PG hydrolase, RipC, by the FtsX extracellular domain (ECD), a ubiquitous transmembrane component of the divisome. RipC control is remarkable for the enormous conformational change encompassing the N- and C-terminal domains. The FtsX–ECD crystal structure shows not only the RipC binding site—which we confirm in vitro and in vivo—but also the flexibility of the site that provides a potential basis to control RipC affinity. Our results expand and sharpen the FtsX paradigm for regulation of PG hydrolysis.
Multiscale observations of CO
2
,
13
CO
2
, and pollutants at Four Corners for emission verification and attribution
Authors: Lindenmaier Rodica , Dubey Manvendra K. , Henderson Bradley G. , Butterfield Zachary T. , Herman Jay R. , Rahn Thom , Lee Sang-Hyun
Published: May 2014

Significance

Climate change and air pollution caused by fossil-energy-related CO
2
and NO
x
emissions is a capstone societal issue. A critical barrier to an international treaty aimed toward controlling emissions is the inability to verify inventories and reduction of emissions claimed by individual nations following implementation of new technologies. We demonstrate for the first time, to our knowledge, that simultaneous remote observations of CO
2
, NO
2
, and CO regional column enhancements can be made with high fidelity and frequency. These can then be used to identify emissions from power plants and to distinguish them from other sources. Our findings represent a significant advancement in remote sensing monitoring methodology and can be used to develop an enforceable, transparent, and equitable climate treaty.
Trichomonas vaginalis
homolog of macrophage migration inhibitory factor induces prostate cell growth, invasiveness, and inflammatory responses
Authors: Twu Olivia , Dessí Daniele , Vu Anh , Mercer Frances , Stevens Grant C. , de Miguel Natalia , Rappelli Paola , Cocco Anna Rita , Clubb Robert T. , Fiori Pier Luigi , Johnson Patricia J.
Published: May 2014

Significance

Prostate cancer is the most common nonskin cancer in America and the fifth most common cancer worldwide. Inflammation is implicated in the initiation and progression of prostate cancer; however, sources of inflammation remain unidentified.
Trichomonas vaginalis
is a prevalent parasite that infects prostate epithelium and is associated with an increase in aggressive prostate cancer. Here, we demonstrate that a secreted
T. vaginalis
protein homologous to human macrophage migration inhibitory factor elicits antibodies in infected individuals, increases prostate cell proliferation and invasiveness, and induces cellular pathways linked to inflammation. This study demonstrates that a specific parasite-derived protein can mimic its human homolog to increase inflammation and cell proliferation, which, in turn, may result in the promotion and progression of prostate cancer.
Superoxide dismutase deficiency impairs olfactory sexual signaling and alters bioenergetic function in mice
Authors: Garratt Michael , Pichaud Nicolas , Glaros Elias N. , Kee Anthony John , Brooks Robert C.
Published: May 2014

Significance

Oxidative stress is expected to restrict investment in life history traits, including sexual signals used to attract mates. However, evidence supporting this prediction remains equivocal. We utilized superoxide dismutase knockout mice to provide, to our knowledge, the first direct evidence that oxidative stress impairs investment in important sexual signals, in this case major urinary protein pheromones with a well-established role in mate attraction. When males were housed in a competitive social environment, further morphological impairments in sexual signaling were revealed (through smaller preputial glands). Impairments in bioenergetic function, not previously known in this mouse model, also became apparent, highlighting how changes in the housing environment of model organisms can reveal previously undiscovered traits of interest.
Humidity sensation requires both mechanosensory and thermosensory pathways in
Caenorhabditis elegans
Authors: Russell Joshua , Vidal-Gadea Andrés G. , Makay Alex , Lanam Carolyn , Pierce-Shimomura Jonathan T.
Published: May 2014

Significance

Although the neurons and molecules that mediate the sensing of light, odors, tastants, temperature, and pressure have been elucidated, how humidity is sensed in most animals remains unclear. We used the experimental amenability of the model nematode
Caenorhabditis elegans
to discover a mechanism for sensing humidity. This worm pairs mechanical and thermal information associated with humidity levels via parallel sensory pathways. This strategy, first proposed more than 100 years ago by Thunberg, is notable for not requiring specialized sensory apparatus (or even hair). Because these neurons and their molecular sensors have equivalents represented in diverse animals, the humidity sensation mechanism that we describe here could be used by many animals, including humans.
Insulin regulates carboxypeptidase E by modulating translation initiation scaffolding protein eIF4G1 in pancreatic β cells
Authors: Liew Chong Wee , Assmann Anke , Templin Andrew T. , Raum Jeffrey C. , Lipson Kathryn L. , Rajan Sindhu , Qiang Guifen , Hu Jiang , Kawamori Dan , Lindberg Iris , Philipson Louis H. , Sonenberg Nahum , Goldfine Allison B. , Stoffers Doris A. , Mirmira Raghavendra G. , Urano Fumihiko , Kulkarni Rohit N.
Published: May 2014

Significance

Elevated circulating proinsulin and a poor biological response to insulin are observed early in individuals with type 2 diabetes. Genome-wide association studies have recently identified genes associated with proinsulin processing, and clinical observations suggest that elevated proinsulin and its intermediates are markers of dysfunctional insulin-secreting β cells. Here, we propose a previously unidentified mechanism in the regulation of an enzyme that is involved in proinsulin processing called carboxypeptidase E (CPE). Disruption of insulin signaling in β cells reduces expression of a scaffolding protein, eukaryotic translation initiation factor 4 gamma 1, that is required for the initiation of translation and occurs via regulation of two transcription factors, namely, pancreatic and duodenal homeobox 1 and sterol regulatory element-binding protein 1. Together, these effects lead to reduced levels of CPE protein and poor proinsulin processing in β cells.
Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses
Authors: Byrd-Leotis Lauren , Liu Renpeng , Bradley Konrad C. , Lasanajak Yi , Cummings Sandra F. , Song Xuezheng , Heimburg-Molinaro Jamie , Galloway Summer E. , Culhane Marie R. , Smith David F. , Steinhauer David A. , Cummings Richard D.
Published: May 2014

Significance

Studies using novel “shotgun glycan microarray” technology identify, for the first time to our knowledge, the endogenous receptors for influenza viruses from a natural host, the pig. Libraries of total N-glycans from pig lung were probed for binding properties using a panel of influenza viruses isolated from humans, birds, and swine. Natural glycan receptors were identified for all viruses examined, and although some displayed the rather broad α2,3 or α2,6 sialic acid linkage specificity conventionally associated with avian or human viruses, other strains were highly specific, revealing a complexity that has not been demonstrated previously. Because pigs are often implicated as intermediate hosts for pandemic viruses, these results and the approaches described will transform our understanding of influenza host range, transmission, and pathogenicity.
Local photic entrainment of the retinal circadian oscillator in the absence of rods, cones, and melanopsin
Authors: Buhr Ethan D. , Van Gelder Russell N.
Published: May 2014

Significance

The physiology of the mammalian retina is governed by a molecular circadian clock. The retina is also the sole photoreceptive tissue for the synchronization of the master circadian clock, the suprachiasmatic nucleus (SCN), to light/dark cycles. The SCN synchronizes the phases of peripheral clocks throughout the body. It is unknown whether the retina is entrained by the SCN, or is directly entrained by light/dark signals. We report that the retinal circadian clock synchronizes directly to light/dark cycles, independent of the SCN phase. Unexpectedly, the retina uses photoreceptors distinct from those used for circadian photoreception or vision for this entrainment.
Anomalies in bulk supercooled water at negative pressure
Authors: Pallares Gaël , El Mekki Azouzi Mouna , González Miguel A. , Aragones Juan L. , Abascal José L. F. , Valeriani Chantal , Caupin Frédéric
Published: May 2014

Significance

Water is the most familiar liquid, and arguably the most complex. Anomalies of supercooled water have been measured during decades, and competing interpretations proposed. Yet, a decisive experiment remains elusive, because of unavoidable crystallization into ice. We investigate the state of water that is both supercooled and under mechanical tension, or negative pressure. Liquids under negative pressure can be found in plants or fluid inclusions in minerals. Using such water inclusions in quartz, we report, to our knowledge, the first measurements on doubly metastable water down to −15°C and around

−
100
 
M
P
a

. We observe sound velocity anomalies that can be reproduced quantitatively with molecular dynamics simulations. These results suggest the possibility to rule out two proposed scenarios for water anomalies, and put further constraints on the remaining ones.
Dynamic JUNQ inclusion bodies are asymmetrically inherited in mammalian cell lines through the asymmetric partitioning of vimentin
Authors: Ogrodnik Mikołaj , Salmonowicz Hanna , Brown Rachel , Turkowska Joanna , Średniawa Władysław , Pattabiraman Sundararaghavan , Amen Triana , Abraham Ayelet-chen , Eichler Noam , Lyakhovetsky Roman , Kaganovich Daniel
Published: May 2014

Significance

We show, for the first time to our knowledge, that vimentin intermediate filaments establish mitotic polarity in dividing mammalian cell lines. By confining damaged, misfolded, and aggregated proteins in JUNQ inclusion bodies, vimentin mediates their asymmetric partitioning during division. We also, to our knowledge, provide the first direct evidence of active proteasomal degradation in dynamic JUNQ inclusion bodies. This work sheds light on an important rejuvenation mechanism in mammalian cells and provides new biological insight into the role of inclusion bodies in regulating aggregation, toxicity, and aging.
Tropospheric winds from northeastern China carry the etiologic agent of Kawasaki disease from its source to Japan
Authors: Rodó Xavier , Curcoll Roger , Robinson Marguerite , Ballester Joan , Burns Jane C. , Cayan Daniel R. , Lipkin W. Ian , Williams Brent L. , Couto-Rodriguez Mara , Nakamura Yosikazu , Uehara Ritei , Tanimoto Hiroshi , Morguí Josep-Anton
Published: May 2014

Significance

Kawasaki disease (KD), the leading cause of acquired heart disease in children worldwide, has remained a mystery for more than 40 y. No etiological agent has yet been identified. By using simulations with the flexible particle dispersion model from different Japanese cities from each single high (low) KD incidence day, the source region KD is retrieved in cereal croplands in northeastern China. We infer the incubation time for KD ranges from 6 h to 2 d, thus favoring an antigenic or toxic exposure as the trigger.
Candida
sp. is reported as the dominant fungal species collected aloft (54% of all fungal DNA clones) demonstrating the potential for human disease in aerosols transported by wind currents traveling long distances.
Dynamics of spontaneous flipping of a mismatched base in DNA duplex
Authors: Yin Yandong , Yang Lijiang , Zheng Guanqun , Gu Chan , Yi Chengqi , He Chuan , Gao Yi Qin , Zhao Xin Sheng
Published: May 2014

Significance

Spontaneous flipping of a single DNA base to an extrahelical position is a fundamental issue in DNA biophysics. The dynamics of such spontaneous flipping of a lesion or mismatched base is an important biophysical feature of DNA to discriminate damaged base from normal Watson–Crick paired ones. It is therefore closely related to repair enzymes' function to recognize base lesions, a mechanism on which almost all organisms rely to maintain their genome integrity. However, it has remained challenging to obtain reliable thermodynamics and kinetics data on this process. By developing experimental and theoretical techniques, we determined the free energy and rates of DNA spontaneous base flipping, providing further insights into its molecular mechanism.
Structure of the pseudokinase–kinase domains from protein kinase TYK2 reveals a mechanism for Janus kinase (JAK) autoinhibition
Authors: Lupardus Patrick J. , Ultsch Mark , Wallweber Heidi , Bir Kohli Pawan , Johnson Adam R. , Eigenbrot Charles
Published: May 2014

Significance

Cytokine signaling is essential for cell growth, hematopoiesis, and immune system function. Cytokine-mediated receptor dimerization induces intracellular activation of receptor-bound Janus kinases (JAKs), which then induce downstream transcriptional responses. We have determined a two-domain crystal structure containing the pseudokinase and kinase domains from the JAK family member TYK2, which identifies an inhibitory interaction interface between the two domains. Cancer-associated mutations found in other JAK family members map to this inhibitory interaction site, whereas analogous mutations in TYK2 cause in vitro activation of the kinase. This study identifies a mechanism for pseudokinase-mediated autoinhibition of the TYK2 kinase domain and suggests a means by which cancer-associated JAK mutations induce aberrant kinase activity.
Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO
2
fixation
Authors: Könneke Martin , Schubert Daniel M. , Brown Philip C. , Hügler Michael , Standfest Sonja , Schwander Thomas , Schada von Borzyskowski Lennart , Erb Tobias J. , Stahl David A. , Berg Ivan A.
Published: May 2014

Significance

CO
2
fixation is the most important biosynthesis process on Earth, enabling autotrophic organisms to synthesize their entire biomass from inorganic carbon at the expense of energy generated by photo- or chemotrophic processes. In the present study we demonstrate an autotrophy pathway that represents the most energy-efficient mechanism for fixing inorganic carbon in the presence of oxygen. This novel variant of the hydroxypropionate/hydroxybutyrate cycle appears to be common in a ubiquitous and abundant group of microorganisms that can thrive in nutrient-limited environments. This discovery offers a biochemical explanation for the remarkable ecological success of the ammonia-oxidizing archaea in extremely nutrient-limited environments typical of most of the open ocean.
Polarization of IRON-REGULATED TRANSPORTER 1 (IRT1) to the plant-soil interface plays crucial role in metal homeostasis
Authors: Barberon Marie , Dubeaux Guillaume , Kolb Cornelia , Isono Erika , Zelazny Enric , Vert Grégory
Published: May 2014

Significance

Plants take up iron from the soil by using a broad spectrum transporter named IRON-REGULATED TRANSPORTER 1 (IRT1). IRT1 mediates influx of potentially toxic elements such as manganese, zinc, cobalt, and cadmium. We uncovered that the localization at the cell surface of IRT1 is directly controlled by its secondary toxic substrates. When these metals are found at low levels in soils, IRT1 is located at the plasma membrane in a polar fashion facing the soil. We identified a lipid-binding protein recruited to endosomes that controls IRT1's dynamics and polarity, and plays an important role in the radial transport of metals. Altogether, our work points to an unexpected mode of radial transport of iron toward vascular tissues involving efflux transporters.
Protection from hypertension in mice by the Mediterranean diet is mediated by nitro fatty acid inhibition of soluble epoxide hydrolase
Authors: Charles Rebecca L. , Rudyk Olena , Prysyazhna Oleksandra , Kamynina Alisa , Yang Jun , Morisseau Christophe , Hammock Bruce D. , Freeman Bruce A. , Eaton Philip
Published: May 2014

Significance

The Mediterranean diet is characterized by consumption of unsaturated fats with vegetables rich in nitrite and nitrate, resulting in endogenous formation of nitro fatty acids. These reactive lipids adduct to soluble epoxide hydrolase, inhibiting it to lower blood pressure. Mice genetically engineered to be resistant to this adductive inhibition had high blood pressure basally and their hydrolase activity was fully resistant to inhibition by nitro fatty acid supplied directly or generated via the Mediterranean diet. Similarly nitro fatty acid lowered blood pressure and abrogated cardiac hypertrophy in a hypertension model in wild-type mice, but was ineffective in mutant mice. Thus, protection from hypertension afforded by the Mediterranean diet is mediated by nitro-fatty acid-dependent inhibition of soluble epoxide hydrolase.
Antagonistic actions of Rcor proteins regulate LSD1 activity and cellular differentiation
Authors: Upadhyay Ghanshyam , Chowdhury Asif H. , Vaidyanathan Bharat , Kim David , Saleque Shireen
Published: May 2014

Significance

This work illustrates the dual regulation of the potent and widely expressed demethylase lysine-specific demethylase 1 (LSD1) by the antagonistic actions of stimulatory and inhibitory Rcor factors and their consequences on hematopoietic differentiation. Given the crucial role of LSD1 in diverse developmental contexts, including ES cells, multiple mammalian tissues, and oncogenesis, these results could potentially reflect the function of LSD1 and Rcor1-3 in multiple normal and aberrant developmental contexts. Moreover, these insights could be used to develop targeted strategies for controlling LSD1 activity in different diseases.
Effect of the Spanish Conquest on coastal change in Northwestern Peru
Authors: Belknap Daniel F. , Sandweiss Daniel H.
Published: May 2014

Significance

Culture contact can lead to unexpected consequences. The population of Peru dropped precipitously after the Spanish Conquest, changing the patterns and intensity of economic activities. In northern Peru, such changes affected the evolution of beach ridges (narrow sand dunes many kilometers long, parallel to the shoreline) north of the Chira River. A similar hiatus in beach ridge formation about 2,800 y ago correlates with increased El Niño frequency, and possibly a local decline in population at that time. This study illustrates the value of comparing historic, archaeological, climatic, and geological data to understand change in coupled natural and human systems.
Mechanism for neutralizing activity by the anti-CMV gH/gL monoclonal antibody MSL-109
Authors: Fouts Ashley E. , Comps-Agrar Laëtitia , Stengel Katharina F. , Ellerman Diego , Schoeffler Allyn J. , Warming Søren , Eaton Dan L. , Feierbach Becket
Published: May 2014

Significance

The CMV glycoprotein (g) entry complex gH/gL is a significant target of the human immune system, eliciting production of highly neutralizing antibodies. MSL-109, a monoclonal antibody that binds to gH, potently neutralizes CMV entry. Here, viral mutants resistant to MSL-109 were generated and the epitope mapped on the model of the structure of CMV gH. We have used a cell-surface fluorescence assay to reveal novel interactions among CMV glycoproteins and probe the effect of MSL-109 on glycoprotein interactions. Our data confirm cross-talk between gH/gL and gB, the fusion protein. Moreover, we identify a homophilic interaction between gH/gL heterodimers that is perturbed by MSL-109. This study suggests a novel mechanism of neutralization, and highlights potential strategies for treatment of CMV disease.
Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing
Authors: Yu Stephanie C. Y. , Chan K. C. Allen , Zheng Yama W. L. , Jiang Peiyong , Liao Gary J. W. , Sun Hao , Akolekar Ranjit , Leung Tak Y. , Go Attie T. J. I. , van Vugt John M. G. , Minekawa Ryoko , Oudejans Cees B. M. , Nicolaides Kypros H. , Chiu Rossa W. K. , Lo Y. M. Dennis
Published: May 2014

Significance

Noninvasive prenatal testing (NIPT) using fetal DNA in maternal plasma has been rapidly adopted worldwide. Current NIPT for fetal chromosomal disorders are based on the counting of DNA molecules in maternal plasma. Here, we show that plasma DNA-based molecular diagnostics can also be built around DNA fragment size, instead of count. First, we demonstrate that the fetal DNA fraction in maternal plasma can be rapidly measured by size analysis, even simply using microchip-based capillary electrophoresis. Second, we show that plasma DNA size analysis can be used for the detection of multiple types of fetal chromosomal aneuploidies with high accuracy. This strategy has many potential diagnostic applications, e.g., in oncology and transplantation monitoring.
Lagging adaptation to warming climate in
Arabidopsis thaliana
Authors: Wilczek Amity M. , Cooper Martha D. , Korves Tonia M. , Schmitt Johanna
Published: May 2014

Significance

If adaptive evolution cannot keep up with rapid climate change, populations and even species may decline or go extinct. Such adaptational lag is predicted, but evidence is scarce. We tested for lagging adaptation to warming climate in banked seeds of the annual weed
Arabidopsis thaliana
in common garden experiments in four sites across the species’ native European climate range. Genotypes originating in climates historically warmer than the planting site had higher relative fitness than native genotypes in every site. This result suggests that local adaptive optima have shifted rapidly with recent climate warming across the species’ native range, and that the potential for adaptational lag deserves consideration in conservation and management decisions for many species.
Golgi and plasma membrane pools of PI(4)P contribute to plasma membrane PI(4,5)P
2
and maintenance of KCNQ2/3 ion channel current
Authors: Dickson Eamonn J. , Jensen Jill B. , Hille Bertil
Published: May 2014

Significance

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P
2
] is a key informational phospholipid, localized to and defining the inner leaflet of the plasma membrane (PM). How PM PI(4,5)P
2
is sourced and regulated is critically important to the understanding of cellular trafficking, cell motility, membrane identity, and ion channel activity. The immediate precursor of PI(4,5)P
2
is PI(4)P. Direct evidence detailing the location and contribution of PI(4)P pool(s) maintaining steady-state PM PI(4,5)P
2
is lacking. We find that PM PI(4,5)P
2
levels are supported by at least two continuously supplying precursor pools of PI(4)P, one in the PM and the other in the Golgi. The contribution of the Golgi pool of PI(4)P highlights the possibility that PM PI(4,5)P
2
production is coupled to important cell biological processes.
Predation-associated modulation of movement-based signals by a Bahamian lizard
Authors: Steinberg David S. , Losos Jonathan B. , Schoener Thomas W. , Spiller David A. , Kolbe Jason J. , Leal Manuel
Published: May 2014

Significance

Communication often is a major component of social interactions. Signaling individuals are faced with the challenge of capturing the attention of intended receivers while limiting eavesdropping by potential predators. We conducted an experiment in nature to evaluate the hypothesis that prey species can modulate the physical properties of movement-based displays in response to the presence of predators. We found that male brown anoles dramatically decreased the amplitude of their head-bob displays in the presence of a predatory lizard, resulting in less conspicuous signals. Although less conspicuous signals may be safer for the signaling individuals, they also reduce the distance from which potential mates or competitors can detect them, which might affect the territory size and reproductive success of signaling males.
Chapter 4. Writing and becoming a scientist
Authors: Lerner Neal , Poe Mya
Published: May 2014

In many communication-intensive (CI) classes in the sciences, students are learning the essential practices for knowledge production in tandem with professional communication practices. In short, they are learning to communicate as a biologist or chemist or physicist. To explore this process more closely, we conducted a three-year qualitative study of 17 undergraduate and graduate students in science and engineering CI classes at the Massachusetts Institute of Technology via initial and end-of-year surveys, one-to-one interviews, classroom observation, and collection and analysis of student writing. In this chapter, we present the findings about three students who were sophomores at the beginning of the study and graduating seniors at its conclusion to understand if these students evidenced changes in their understanding of the roles and purposes of communicating science. Based on coded interview data and analysis of student writing, the case studies we report in this chapter offer insights into the intertwined relationship between students’ developing scientific knowledge and their shifting identities as students/scientists/engineers/writers. Understanding students’ perspectives on entering professional communities through their communicative practices, particularly given the constraints of school contexts, speaks to the need to design instruction that responds to students’ developmental levels and their readiness to learn to communicate in science and engineering.
What typology reveals about modality  in Japanese
Authors: Horie Kaoru , Narrog Heiko
Published: May 2014

This paper presents a functional-typological analysis of three linguistic manifestations of modality-related phenomena in Japanese. When compared with English, German, and Korean, Japanese is characterized by a modal system that encodes event, epistemic, and evidential modalities, and a relatively impoverished grammatical mood, as well as a rich discourse system of sentence-final particles that can be grouped into speaker-oriented and hearer-oriented particles. The modality system in Japanese demonstrates a relatively high degree of elaboration in formal coding of evidential and discourse modalities. The cross-linguistic differences in the degrees of elaboration among different subcategories of modality as presented in this study require an explanation beyond the confines of grammar to find a link between grammar and other cognitive and communicative systems.
Producing scientific knowledge on migration: perspectives on African and Arab countries
Authors: Kabbanji Lama
Published: May 2014

The general objective of this paper is to explore the scientific knowledge produced on the topic of migration in/from African or Arab countries. More specifically, it attempts to identify how different features of the current international division of scientific labour can be illustrated by an examination of the research conducted on migration in/from African and Arab countries. Two main aspects are explored: the role that Arab and African academic communities play in the production of knowledge on migration; and the research priorities among ‘Western and non-Western’ academics. Articles published between the years 2000 and 2010 in three main journals specialized in migration studies are analysed in order to discuss to a certain extent the setting of a hegemonic scientific agenda on international migration which mainly reflects West European and North American concerns. Two main conclusions are drawn: (1) the quasiabsence of scholars from Arab and African academic institutions in mainstream journals is one of the factors explaining the focus of published research on topics relevant to ‘Western’ societies (mainly the insertion process in European and North American countries); and (2) important dimensions of migration dynamics in Arab and African countries are being neglected.