bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
Authors: Boiteux Céline , Vorobyov Igor , French Robert J. , French Christopher , Yarov-Yarovoy Vladimir , Allen Toby W. 
Published: August 2014

SignificanceVoltage-gated sodium (Nav) channels control neuronal signaling and are key targets for local anesthetics, antiepileptics, and therapeutics for a range of disorders. Multimicrosecond Anton simulations have provided completely unbiased molecular-level views of the interactions of lipophilic drugs with the recently solved bacterial channel, NavAb fromArcobacter butzleri. Newly parameterized benzocaine and phenytoin molecules exhibit different membrane partition coefficients, crossing rates and distributions around the channel, leading to the identification of distinct high- and low-affinity sites. We observe a minimum free energy pathway through membrane-bound fenestrations to a pore-blocking location, or from aqueous solution directly through the (closed) intracellular gate. These observations help explain experimental data and provide insight into Navinhibition processes that will assist future drug development.
Adaptive optoelectronic camouflage systems with designs inspired by cephalopod skins
Authors: Yu Cunjiang , Li Yuhang , Zhang Xun , Huang Xian , Malyarchuk Viktor , Wang Shuodao , Shi Yan , Gao Li , Su Yewang , Zhang Yihui , Xu Hangxun , Hanlon Roger T. , Huang Yonggang , Rogers John A. 
Published: August 2014

Significance
Artificial systems that replicate functional attributes of the skins of cephalopods could offer capabilities in visual appearance modulation with potential utility in consumer, industrial, and military applications. Here we demonstrate a complete set of materials, components, fabrication approaches, integration schemes, bioinspired designs, and coordinated operational modes for adaptive optoelectronic camouflage sheets. These devices are capable of producing black-and-white patterns that spontaneously match those of the surroundings, without user input or external measurement. Systematic experimental, computational, and analytical studies of the optical, electrical, thermal, and mechanical properties reveal the fundamental aspects of operation and also provide quantitative design guidelines that are applicable to future embodiments.
A wave-mechanical model of incoherent quasielastic scattering in complex systems
Authors: Frauenfelder Hans , Fenimore Paul W. , Young Robert D. 
Published: August 2014

SignificanceQuasielastic incoherent neutron scattering (QENS) is a key tool for the exploration of complex systems, such as liquids, polymers, glasses, and biomolecules. A considerable number of neutron facilities exist and more are being planned. Understanding QENS is important, both for comprehending and applying the science and making efficient use of the facilities. We claim that the present explanation of QENS is incomplete. We propose a wave-mechanical model, consistent with neutron diffraction. It is based on the free-energy landscape and treats the neutrons as de Broglie wave packets. The model is supported by experiments and has predictive power. It provides significant insight into the dynamics of proteins and may lead to a better understanding of biological processes.
Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam
Authors: Sawaya Michael R. , Cascio Duilio , Gingery Mari , Rodriguez Jose , Goldschmidt Lukasz , Colletier Jacques-Philippe , Messerschmidt Marc M. , Boutet Sébastien , Koglin Jason E. , Williams Garth J. , Brewster Aaron S. , Nass Karol , Hattne Johan , Botha Sabine , Doak R. Bruce , Shoeman Robert L. , DePonte Daniel P. , Park Hyun-Woo , Federici Brian A. , Sauter Nicholas K. , Schlichting Ilme , Eisenberg David S. 
Published: August 2014

Significance
In vivo microcrystals have been observed in prokaryotic and eukaryotic cells. With rare exception, however, the ∼100,000 biological structures determined by X-ray crystallography to date have required the macromolecule under study to be extracted from the cells that produced it and crystallized in vitro. In vivo crystals present a challenge for structure determination and pose the question of the extent to which in vivo macromolecular structures are similar to those of extracted and recrystallized macromolecules. Here we show that serial femtosecond crystallography enabled by a free-electron laser yields the structure of in vivo crystals, as they exist in a living cell, and in this case the in vivo structure is essentially identical to the structure of extracted and recrystallized protein.
A sharp T-cell antigen receptor signaling threshold for T-cell proliferation
Authors: Au-Yeung Byron B. , Zikherman Julie , Mueller James L. , Ashouri Judith F. , Matloubian Mehrdad , Cheng Debra A. , Chen Yiling , Shokat Kevan M. , Weiss Arthur 
Published: August 2014

SignificanceBiochemical signals triggered by the T-cell receptor (TCR) are required for stimulating T cells and can be initiated within seconds. However, a hallmark of T-cell activation, cell division, occurs hours after TCR signaling has begun, implying that T cells require a minimum duration and/or accumulate TCR signaling events to drive proliferation. To visualize the accumulated signaling experienced by T cells, we used a fluorescent reporter gene that is activated by TCR stimulation. This technique showed a threshold between dividing and nondividing T cells for TCR signaling that does not change with stronger or weaker TCR signaling or the presence of growth factor. Together these data may have implications for the development of T-cell–targeted therapies for autoimmunity.
Immune evasion mediated by tumor-derived lactate dehydrogenase induction of NKG2D ligands on myeloid cells in glioblastoma patients
Authors: Crane Courtney A. , Austgen Kathryn , Haberthur Kristen , Hofmann Carly , Moyes Kara White , Avanesyan Lia , Fong Lawrence , Campbell Michael J. , Cooper Stewart , Oakes Scott A. , Parsa Andrew T. , Lanier Lewis L. 
Published: August 2014

Significance
This study describes a mechanism of immune escape in which glioblastoma cells produce a soluble protein, lactate dehydrogenase 5 (LDH5), that induces the expression of Natural killer group 2, member D (NKG2D) ligands on the surface of healthy myeloid cells. Expression of NKG2D ligands by myeloid cells causes the down-modulation of the activating NKG2D receptor on natural killer cells, thereby preventing their recognition of NKG2D ligand-bearing tumors and impairing their ability to attack and eliminate tumors. The discovery that monocytes in patients with several types of cancer also express NKG2D ligands suggests that LDH5 production by tumors may represent a common mechanism of immune evasion. Blocking LDH5 might improve recognition of tumors in cancer patients.
Milky Way mass galaxies with X-shaped bulges are not rare in the local Universe
Authors: Laurikainen E. , Salo H. , Athanassoula E. , Bosma A. , Herrera-Endoqui M. 
Published: August 2014

Abstract
Boxy/Peanut/X-shaped (B/P/X) bulges are studied using the 3.6 μm images from the Spitzer Survey of Stellar Structure in Galaxies, and the Ks-band images from the Near-IR S0 galaxy Survey. They are compared with the properties of barlenses, defined as lens-like structures embedded in bars, with sizes of ∼50 per cent of bars and axial ratios of ∼0.6–0.9. Based on observations (extending Laurikainen et al.) and recent simulation models, we show evidence that barlenses are the more face-on counterparts of B/P/X-shaped bulges. Using unsharp masks 18 new X-shaped structures are identified, covering a large range of galaxy inclinations. The similar masses and red B−3.6 μm colours of the host galaxies, and the fact that the combined axial ratio distribution of the host galaxy discs is flat, support the interpretation that barlenses and X-shapes are physically the same phenomenon. In Hubble types −3 ≤ T ≤ 2 even half of the bars contain either a barlens or an X-shaped structure. Our detailed 2D multicomponent decompositions for 29 galaxies, fitting the barlens/X-shape with a separate component, indicate very small or non-existent classical bulges. Taking into account that the structures we study have similar host galaxy masses as the Milky Way (MW), our results imply that MW mass galaxies with no significant classical bulges are common in the nearby Universe.
Infliximab Therapy in Pediatric Patients 7 Years of Age and Younger
Authors: Kelsen Judith R. , Grossman Andrew B. , Pauly‐Hubbard Helen , Gupta Kernika , Baldassano Robert N. , Mamula Petar 
Published: August 2014

ABSTRACTBackground:Infliximab (IFX) is efficacious for induction and maintenance of remission in pediatric patients with moderate‐to‐severe inflammatory bowel disease (IBD). It has, however, not been studied in patients 7 years old and younger. Our aim was to characterize efficacy and safety of IFX therapy in this cohort.Methods:This was a retrospective study of patients with IBD ages 7 years and younger, treated with IFX between 1999 and 2011. Medical records were reviewed for age of diagnosis, disease phenotype, therapy, surgery, IFX infusion dates, dose, and intervals. Outcome measures included physician global assessment, corticosteroid requirement, and adverse events.Results:Thirty‐three children (ages 2.4–7 years) were included. Twenty patients had Crohn disease, 4 had ulcerative colitis, and 9 had indeterminate colitis. Maintenance of IFX therapy at 1, 2, and 3 years was 36%, 18%, and 12%, respectively. Patients of age 5 years and younger had the lowest rates of maintenance of therapy at 25% at year 1, and 10% at years 2 and 3 combined. Nine percent of all of the patients demonstrated response measured by the physician global assessment and were steroid free at 1 year. There were 8 infusion reactions. There were no malignancies, serious infections, or deaths.Conclusions:IFX demonstrated a modest response rate and a low steroid‐sparing effect in patients with IBD 7 years old and younger. Although this is a limited study, there appears to be a trend for decreased sustained efficacy with IFX in this age group, particularly in children 5 years old and younger, when compared with the previously published literature in older children.
Branching Out in Roots: Uncovering Form, Function, and Regulation
Authors: Atkinson Jonathan A. , Rasmussen Amanda , Traini Richard , Voß Ute , Sturrock Craig , Mooney Sacha J. , Wells Darren M. , Bennett Malcolm J. 
Published: August 2014

Abstract
Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postembryonic root organogenesis exist in angiosperms. In cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. In this Update, we initially describe the diversity of postembryonic root forms. Next, we review recent advances in our understanding of the genes, signals, and mechanisms regulating lateral root and adventitious root branching in the plant models Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). While many common signals, regulatory components, and mechanisms have been identified that control the initiation, morphogenesis, and emergence of new lateral and adventitious root organs, much more remains to be done. We conclude by discussing the challenges and opportunities facing root branching research.
Radial Transport of Nutrients: The Plant Root as a Polarized Epithelium
Authors: Barberon Marie , Geldner Niko 
Published: August 2014

Abstract
In higher plants, roots acquire water and soil nutrients and transport them upward to their aerial parts. These functions are closely related to their anatomical structure; water and nutrients entering the root first move radially through several concentric layers of the epidermis, cortex, and endodermis before entering the central cylinder. The endodermis is the innermost cortical cell layer that features rings of hydrophobic cell wall material called the Casparian strips, which functionally resemble tight junctions in animal epithelia. Nutrient uptake from the soil can occur through three different routes that can be interconnected in various ways: the apoplastic route (through the cell wall), the symplastic route (through cellular connections), and a coupled trans-cellular route (involving polarized influx and efflux carriers). This Update presents recent advances in the radial transport of nutrients highlighting the coupled trans-cellular pathway and the roles played by the endodermis as a barrier.
Experimentally linking disturbance, resources and productivity to diversity in forest ground‐layer plant communities
Authors: Burton Julia I. , Mladenoff David J. , Forrester Jodi A. , Clayton Murray K. 
Published: August 2014

Summary

Disturbance can function to maintain diversity within forest communities; however, specific mechanisms and the relationship to productivity are not well understood.

We examined these linkages in forest ground‐layer plant communities using a replicated, manipulative field experiment. Treatments included a range of gap sizes and untreated controls. We assessed spatial and temporal responses over the first three years following gap creation.

Light transmittance and soil water content increased with gap size, while rates of colonization and species richness increased after a critical threshold. Subsequent increases in productivity were associated with declines in species richness, increased rates of local extirpation and a unimodal relationship between species richness and productivity at the individual quadrat scale (4 m2).

The richness and productivity of vines, shrubs and especially graminoids, increased within 200–380 m2 gaps treatments. However, the productivity of forbs and tree seedlings did not, showing possible drought sensitivity overriding treatments. Spatial and temporal partitioning of gaps occurred as a result of interactions between species traits and environmental conditions. Significantly, productivity and richness showed complex relationships with canopy structure.

Synthesis. Our results show that richness increases to an asymptote after a critical threshold in disturbance severity initially. Decreases in species richness over time associated with increases in productivity may eventually result in the unimodal relationship predicted by the intermediate disturbance hypothesis. However, species composition continues to differ with canopy gap size, suggesting a range of canopy gap sizes is required to maintain the greatest diversity of plant species over broader spatial and temporal scales.
Korean Television Dramas and the Political Economy of City Promotion
Authors: Oh Youjeong 
Published: August 2014

AbstractThis article examines the ways in which urban processes are associated with the production of culture. It does so by exploring how Korean cities sponsor drama. The historically conditioned and economically neglected status of regional cities, combined with elected local leaders' desire to promote their own areas, has led to a strategy to publicize them by leveraging the popularity of Korean television dramas in Asia. Two distinct types of drama sponsorship by cities — the construction of outdoor settings for drama and ‘city placement’ — manifest the interactions between story‐making and place‐making. The affective process that blends city sites with the characters, storylines and emotional flows of TV drama imbues those sites with a dramatic quality that stimulates the audience's empathy and persuasively motivates them to actually visit the places they have seen televised. Thanks to the broad penetration of television drama, sponsorship by cities has strikingly boosted drama‐driven tourism. Nevertheless, reflecting the speculative nature of TV drama, city promotion through this medium has had limited stability and sustainability. In sum, this article demonstrates that the production of Korean television dramas is deeply associated with the material and spatial conditions in Korean cities.
Recent Advances in Data Mining Techniques and Their Applications in Hyperspectral Image Processing for the Food Industry
Authors: Dai Qiong , Sun Da‐Wen , Xiong Zhenjie , Cheng Jun‐Hu , Zeng Xin‐An 
Published: August 2014

AbstractHyperspectral imaging (HSI) facilitates better characterization of intrinsic and extrinsic properties of foods by integrating traditional spectral and image techniques, in which careful and sophisticated data processing plays an important role. In the past decade, much progress has been made on applying various algorithms to deal with hyperspectral images. This review first introduces the general procedure of hyperspectral data analysis and then illustrates the most typically and commonly used algorithms for denoising, feature selection, model establishment, and evaluation, as well as their applications for assessing food quality, safety, and authenticity. Finally, brief summaries for regression and classification methods are presented. This article will provide a guideline for data mining in the future development of HSI in the food field.
Solid‐State Protein–Carbohydrate Interactions and Their Application in the Food Industry
Authors: Soltanizadeh Nafiseh , Mirmoghtadaie Leila , Nejati Fatemeh , Najafabadi Leila Izadi , Heshmati Maryam Khakbaz , Jafari Maryam 
Published: August 2014

AbstractThe growing interest in food component interactions, especially the solid‐state protein–carbohydrate ones, has led to a growing body of knowledge on the effects of these interactions on the physical, chemical, and structural properties of compositionally complex food systems. The goal of the present review is to survey the critical mechanisms involved in protein–carbohydrate interactions as a key step toward the rational formulation and processing of protein‐ and carbohydrate‐rich foods to produce products with desirable properties without adverse reactions. The hypotheses proposed on the stabilizing effects of carbohydrates on proteins and the role of different types of sugars in the extent of these interactions are reviewed in this article. Another aspect of this review involves the successful drying of proteins by spray‐drying, freeze‐drying, and supercritical‐fluid‐drying using carbohydrates. Finally, applications of these interesting phenomena to produce important food products including milk powder, infant formulas, bakery products, and fruit and vegetable juice powders are investigated.
Listeria monocytogenes in Aquatic Food Products—A Review
Authors: Jami Mansooreh , Ghanbari Mahdi , Zunabovic Marija , Domig Konrad J. , Kneifel Wolfgang 
Published: August 2014

AbstractWith the increased demand for lightly preserved and/or ready‐to‐eat (RTE) food products, the prevalence of the foodborne pathogen Listeria monocytogenes has increased, which is a public health concern. The goal for this review is to discuss the incidence, epidemiological importance, and contamination routes of L. monocytogenes in various aquatic ecosystems, seafood products, and processing environments and to summarize the data obtained since the 1990s. L. monocytogenes primarily enters the food‐production chain by cross‐contamination in production plants, making this pathogen a major threat to the seafood industry. This pathogen generally contaminates food products at low or moderate levels, but the levels involved in listeriosis outbreaks are significantly higher. The majority of isolates from aquatic products belong to serotype 1/2a, and outbreaks have been linked to highly similar or even indistinguishable strains. Several seafood‐processing plants are colonized by specific “in‐house” flora containing special DNA subtypes of L. monocytogenes. In such cases, L. monocytogenes populations can persist and/or multiply despite the inherent obstacles to their growth in food preservation and manufacturing operations. Therefore, food‐processing facilities must be designed carefully with an emphasis on effective cleaning and disinfecting operations in the production line.
Irradiation for Mold and Mycotoxin Control: A Review
Authors: Calado Thalita , Venâncio Armando , Abrunhosa Luís 
Published: August 2014

AbstractThe mycotoxin issue requires constant vigilance from economic, regulatory, and scientific agents to minimize its toxicological effects on human and animals. The implementation of good practices to avoid fungal growth and mycotoxin production on agricultural commodities is essential to achieve most restrictive safety standards; however, the contribution of novel technologies that may act on postharvesting and poststorage situations may be equally important. Several methodologies, more or less technologically advanced, may be used for this purpose. In this work, we review the role, contribution, and impact of irradiation technology to control the presence of fungi and mycotoxins in food and in feed. The effect of this technology on the viability of mold spores and on the elimination of mycotoxins is reviewed. A critical evaluation of the advantages and disadvantages of irradiation in this context is presented.
Gas Chromatography‐Combustion‐Isotope Ratio Mass Spectrometry for Traceability and Authenticity in Foods and Beverages
Authors: van Leeuwen Katryna A. , Prenzler Paul D. , Ryan Danielle , Camin Federica 
Published: August 2014

AbstractAs consumers demand more certainty over where their food and beverages originate from and the genuineness of ingredients, there is a need for analytical techniques that are able to provide data on issues such as traceability, authenticity, and origin of foods and beverages. One such technique that shows enormous promise in this area is gas chromatography‐combustion‐isotope ratio mass spectrometry (GC‐C‐IRMS). As will be demonstrated in this review, GC‐C‐IRMS is able to be applied to a wide array of foods and beverages generating data on key food components such as aroma compounds, sugars, amino acids, and carbon dioxide (in carbonated beverages). Such data can be used to determine synthetic and natural ingredients; substitution of 1 ingredient for another (such as apple for pear); the use of synthetic or organic fertilizers; and origin of foods and food ingredients, including carbon dioxide. Therefore, GC‐C‐IRMS is one of the most powerful techniques available to detect fraudulent, illegal, or unsafe practices in the food and beverages industries and its increasing use will ensure that consumers may have confidence in buying authentic products of known origin.
Formation, Degradation, and Detoxification of Putrescine by Foodborne Bacteria: A Review
Authors: Wunderlichová Leona , Buňková Leona , Koutný Marek , Jančová Petra , Buňka František 
Published: August 2014

AbstractBiogenic amines (BAs) represent a considerable toxicological risk in some food products. Putrescine is one of the most common BAs in food. Its increased occurrence in food may lead to alimentary poisoning, due to enhancement of the toxic effects of other BAs, and also to lower quality of food, this amine is potentially carcinogenic. Increased occurrence of putrescine in food is mainly due to the bacterial metabolism of the Gram‐negative as well as Gram‐positive bacteria present. The bacterial metabolism of putrescine is very specific due to its complexity (in comparison with the metabolism of other BAs). There are 3 distinct known pathways leading toward the formation of putrescine, in some splices involving up to 6 different enzymes. The existence of more metabolic pathways and the possibility of their simultaneous use by different bacteria complicate the specification of the best conditions for food production and storage, which could lead to a lower content of putrescine. This review provides a summary of the existing knowledge about putrescine production and detection (mainly detection of specific genes for different enzymes using polymerase chain reaction) in both starter and contaminating microorganisms. Thus, this comprehensive review gives a useful overview for further research.