bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesenchymal stem cells: environmentally responsive therapeutics for regenerative medicine
Authors: Murphy Matthew B , Moncivais Kathryn , Caplan Arnold I 
Published: November 2013

AbstractMesenchymal stem cells (MSCs) are partially defined by their ability to differentiate into tissues including bone, cartilage and adipose in vitro, but it is their trophic, paracrine and immunomodulatory functions that may have the greatest therapeutic impact in vivo. Unlike pharmaceutical treatments that deliver a single agent at a specific dose, MSCs are site regulated and secrete bioactive factors and signals at variable concentrations in response to local microenvironmental cues. Significant progress has been made in understanding the biochemical and metabolic mechanisms and feedback associated with MSC response. The anti-inflammatory and immunomodulatory capacity of MSC may be paramount in the restoration of localized or systemic conditions for normal healing and tissue regeneration. Allogeneic MSC treatments, categorized as a drug by regulatory agencies, have been widely pursued, but new studies demonstrate the efficacy of autologous MSC therapies, even for individuals affected by a disease state. Safety and regulatory concerns surrounding allogeneic cell preparations make autologous and minimally manipulated cell therapies an attractive option for many regenerative, anti-inflammatory and autoimmune applications.
Three-dimensional optical holography using a plasmonic metasurface
Authors: Huang Lingling , Chen Xianzhong , Mühlenbernd Holger , Zhang Hao , Chen Shumei , Bai Benfeng , Tan Qiaofeng , Jin Guofan , Cheah Kok-Wai , Qiu Cheng-Wei , Li Jensen , Zentgraf Thomas , Zhang Shuang 
Published: November 2013

AbstractBenefitting from the flexibility in engineering their optical response, metamaterials have been used to achieve control over the propagation of light to an unprecedented level, leading to highly unconventional and versatile optical functionalities compared with their natural counterparts. Recently, the emerging field of metasurfaces, which consist of a monolayer of photonic artificial atoms, has offered attractive functionalities for shaping wave fronts of light by introducing an abrupt interfacial phase discontinuity. Here we realize three-dimensional holography by using metasurfaces made of subwavelength metallic nanorods with spatially varying orientations. The phase discontinuity takes place when the helicity of incident circularly polarized light is reversed. As the phase can be continuously controlled in each subwavelength unit cell by the rod orientation, metasurfaces represent a new route towards high-resolution on-axis three-dimensional holograms with a wide field of view. In addition, the undesired effect of multiple diffraction orders usually accompanying holography is eliminated.
A comparison and optimization of methods and factors affecting the transformation of Escherichia coli
Authors: Chan Weng-Tat , Verma Chandra S. , Lane David P. , Gan Samuel Ken-En 
Published: November 2013

DNA manipulation routinely requires competent bacteria that can be made using one of numerous methods. To determine the best methods, we compared four commonly used chemical methods (DMSO, MgCl2–CaCl2, CaCl2 and Hanahan's methods) on frequently used Escherichia coli (E. coli) strains: DH5α, XL-1 Blue, SCS110, JM109, TOP10 and BL21-(DE3)-PLysS. Hanahan's method was found to be most effective for DH5α, XL-1 Blue and JM109 strains (P&lt;0.05), whilst the CaCl2 method was best for SCS110, TOP10 and BL21 strains (P&lt;0.05). The use of SOB (super optimal broth) over LB [Luria–Bertani (broth)] growth media was found to enhance the competency of XL-1 Blue (P&lt;0.05), dampened JM109′s competency (P&lt;0.05), and had no effect on the other strains (P&gt;0.05). We found no significant differences between using 45 or 90 s heat shock across all the six strains (P&gt;0.05). Through further optimization by means of concentrating the aliquots, we were able to get further increases in transformation efficiencies. Based on the optimized parameters and methods, these common laboratory E. coli strains attained high levels of TrE (transformation efficiency), thus facilitating the production of highly efficient and cost-effective competent bacteria.
ISCB: past–present perspective for the International Society for Computational Biology
Authors: Rost Burkhard 
Published: November 2013

Abstract
Since its establishment in 1997, International Society for Computational Biology (ISCB) has contributed importantly toward advancing the understanding of living systems through computation. The ISCB represents nearly 3000 members working in &gt;70 countries. It has doubled the number of members since 2007. At the same time, the number of meetings organized by the ISCB has increased from two in 2007 to eight in 2013, and the society has cemented many lasting alliances with regional societies and specialist groups. ISCB is ready to grow into a challenging and promising future. The progress over the past 7 years has resulted from the vision, and possibly more importantly, the passion and hard working dedication of many individuals.
footprintDB: a database of transcription factors with annotated cis elements and binding interfaces
Authors: Sebastian Alvaro , Contreras-Moreira Bruno 
Published: November 2013

Abstract
Motivation: Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases.
Results: FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value.
Availability and implementation: Web site implemented in PHP, Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.
Contact: bioquimicas@yahoo.es; bcontreras@eead.csic.es
Supplementary information: Supplementary data are available at Bioinformatics online.
Primary Care Guidelines for the Management of Persons Infected With HIV: 2013 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Aberg Judith A. , Gallant Joel E. , Ghanem Khalil G. , Emmanuel Patricia , Zingman Barry S. , Horberg Michael A. 
Published: November 2013

Abstract
Evidence-based guidelines for the management of persons infected with human immunodeficiency virus (HIV) were prepared by an expert panel of the HIV Medicine Association of the Infectious Diseases Society of America. These updated guidelines replace those published in 2009. The guidelines are intended for use by healthcare providers who care for HIV-infected patients. Since 2009, new antiretroviral drugs and classes have become available, and the prognosis of persons with HIV infection continues to improve. However, with fewer complications and increased survival, HIV-infected persons are increasingly developing common health problems that also affect the general population. Some of these conditions may be related to HIV infection itself or its treatment. HIV-infected persons should be managed and monitored for all relevant age- and sex-specific health problems. New information based on publications from the period 2009–2013 has been incorporated into this document.
Novel functional APOB mutations outside LDL-binding region causing familial hypercholesterolaemia
Authors: Alves Ana Catarina , Etxebarria Aitor , Soutar Anne Katherine , Martin Cesar , Bourbon Mafalda 
Published: November 2013

AbstractFamilial hypercholesterolaemia (FH) is characterized by increased circulating low-density lipoprotein (LDL) cholesterol leading to premature atherosclerosis and coronary heart disease. Although FH is usually caused by mutations in LDLR, mutations in APOB and PCSK9 also cause FH but only a few mutations have been reported, APOB p.R3527Q being the most common. However, 30–80% of clinical FH patients do not present an identifiable mutation in any of the described genes. To identify the genetic cause of the hypercholesterolaemia in 65 patients without mutations in LDLR, PCSK9 or in fragments of exon 26 and 29 of APOB currently analysed, we performed whole sequencing of APOB by pyrosequencing. A total of 10 putative mutations in APOB were identified. Flow cytometry with fluorescently labelled LDL from patients and relatives showed that p.Arg1164Thr (exon 22) and p.Gln4494del (exon 29) presented a 40% decrease in internalization in lymphocytes and HepG2 cells, very similar to APOB3527. The proliferation assays with U937 cells showed reduced growth for both cases. The variant p.Tyr1247Cys was found to be neutral and other three alterations were considered polymorphisms. Our results emphasize the need to study the whole APOB in routine protocols to improve patient identification and cardiovascular risk assessment.
Genetic marking of farmed Atlantic cod (Gadus morhua l.) and detection of escapes from a commercial cod farm
Authors: Jørstad Knut E. , Otterå Håkon , van der Meeren Terje , Dahle Geir , Paulsen Ole I. , Bakke Gunnar , Svåsand Terje 
Published: November 2013

Abstract
A genetically marked Atlantic cod (Gadus morhua L.) strain was used to identify escapes from commercial cod farms, and to investigate the potential interbreeding between farmed and wild cod. This farmed cod was homozygote for a rare allele (30) in the GPI-1 locus expressed in white muscle tissue. Juveniles were produced from this strain in 2007 and 2008, and 500 000 individuals of each year class were transported to a cod farm in western Norway, where they were raised under commercial conditions. A monitoring fishing program was established from spring 2007 to detect escapees during the farming period. The first farmed cod escapees, identified to the 2007 year class through the genetic mark, age and body size, were detected during the fishing survey in November 2008. The second escape of the same year class was detected during the natural spawning season in early April 2009. A third escape was detected in November 2009, and this time the farmed cod were identified to the 2008 year class. The escapees were spreading through the whole fjord system, including local spawning sites for wild cod. Detailed examination of the escaped cod revealed a substantial degree of sexual maturation, and nearly 1000 cod larvae and early juveniles were therefore collected through spring 2009. The genetic analyses identified eight of these as genetically marked, demonstrating successful reproduction either in the cage or after escape. Interbreeding between escaped and wild cod may also have occurred, but cannot be proven from our material. In all years after the three identified escapes, genetically marked cod were found in the fjord area. In addition, several specimens were observed in adjacent fjord systems, demonstrating long-term survival in the local spawning areas as well as substantial spread over larger distances.
An econometric analysis of the Spanish fresh fish market
Authors: Castillo-Manzano José I. , López-Valpuesta Lourdes , Gonzalez-Laxe Fernando , Pedregal Diego J. 
Published: November 2013

AbstractThis article seeks to analyse the factors that determine the dynamics of the balance between supply and demand in the Spanish fresh fish market. For this, the time-series of fresh fish landed in the 1973–2009 period is analysed through an estimation of the series of transfer function models. Among other things, the findings in the Spanish case show a complex relationship between the amount of fish landed and price; a clear substitution relationship between fresh fish and aquaculture; a negative impact of labour costs in a manual labour-intensive sector such as fishing, which in developed countries is being affected by an exodus of manpower to other sectors where there is less uncertainty surrounding labour conditions; the impact of Spain being barred from international fishing grounds a result of the delimitation of exclusive economic zones (EEZs); and the dwindling importance of fisheries traffic as a result of the port devolution process begun in Spain in the early 1990s. The non-significance of a priori key factors, such as the price of oil and Spain's entry into the EEC, can be explained by widespread energy subsidies and contradictions in the objectives of the Common Fisheries Policy, respectively.
Glitch recoveries in radio-pulsars and magnetars
Authors: Haskell B. , Antonopoulou D. 
Published: November 2013

Abstract
Pulsar glitches are sudden increases in the spin frequency of an otherwise steadily spinning down neutron star. These events are thought to represent a direct probe of the dynamics of the superfluid interior of the star. However glitches can differ significantly from one another, not only in size and frequency, but also in the post-glitch response of the star. Some appear as simple steps in frequency, while others also display an increase in spin-down rate after the glitch. Others still show several exponentially relaxing components in the post-glitch recovery. We show that if glitches are indeed due to large-scale unpinning of superfluid vortices, the different regions in which this occurs and respective time-scales on which they recouple can lead to the various observed signatures. Furthermore, we show that this framework naturally accounts for the peculiar relaxations of glitches in Anomalous X-ray Pulsars.
Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork
Authors: Yuan Quan , McHenry Charles S. 
Published: November 2013

Abstract
Two models have been proposed for triggering release of the lagging strand polymerase at the replication fork, enabling cycling to the primer for the next Okazaki fragment—either collision with the 5′-end of the preceding fragment (collision model) or synthesis of a new primer by primase (signaling model). Specific perturbation of lagging strand elongation on minicircles with a highly asymmetric G:C distribution with ddGTP or dGDPNP yielded results that confirmed the signaling model and ruled out the collision model. We demonstrated that the presence of a primer, not primase per se, provides the signal that triggers cycling. Lagging strand synthesis proceeds much faster than leading strand synthesis, explaining why gaps between Okazaki fragments are not found under physiological conditions.
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
Authors: Espah Borujeni Amin , Channarasappa Anirudh S. , Salis Howard M. 
Published: November 2013

Abstract
The ribosome’s interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5′ untranslated regions (5′ UTRs) are commonly found in bacterial mRNAs, though the physical mechanisms that determine how the ribosome binds these upstream regions remain poorly defined. Here, we systematically investigate the ribosome’s interactions with structured standby sites, upstream of Shine–Dalgarno sequences, and show that these interactions can modulate translation initiation rates by over 100-fold. We find that an mRNA’s translation initiation rate is controlled by the amount of single-stranded surface area, the partial unfolding of RNA structures to minimize the ribosome’s binding free energy penalty, the absence of cooperative binding and the potential for ribosomal sliding. We develop a biophysical model employing thermodynamic first principles and a four-parameter free energy model to accurately predict the ribosome’s translation initiation rates for 136 synthetic 5′ UTRs with large structures, diverse shapes and multiple standby site modules. The model predicts and experiments confirm that the ribosome can readily bind distant standby site modules that support high translation rates, providing a physical mechanism for observed context effects and long-range post-transcriptional regulation.
Modification of Plasma Membrane Organization in Tobacco Cells Elicited by Cryptogein
Authors: Gerbeau-Pissot Patricia , Der Christophe , Thomas Dominique , Anca Iulia-Andra , Grosjean Kevin , Roche Yann , Perrier-Cornet Jean-Marie , Mongrand Sébastien , Simon-Plas Françoise 
Published: November 2013

AbstractLipid mixtures within artificial membranes undergo a separation into liquid-disordered and liquid-ordered phases. However, the existence of this segregation into microscopic liquid-ordered phases has been difficult to prove in living cells, and the precise organization of the plasma membrane into such phases has not been elucidated in plant cells. We developed a multispectral confocal microscopy approach to generate ratiometric images of the plasma membrane surface of Bright Yellow 2 tobacco (Nicotiana tabacum) suspension cells labeled with an environment sensitive fluorescent probe. This allowed the in vivo characterization of the global level of order of this membrane, by which we could demonstrate that an increase in its proportion of ordered phases transiently occurred in the early steps of the signaling triggered by cryptogein and flagellin, two elicitors of plant defense reactions. The use of fluorescence recovery after photobleaching revealed an increase in plasma membrane fluidity induced by cryptogein, but not by flagellin. Moreover, we characterized the spatial distribution of liquid-ordered phases on the membrane of living plant cells and monitored their variations induced by cryptogein elicitation. We analyze these results in the context of plant defense signaling, discuss their meaning within the framework of the “membrane raft” hypothesis, and propose a new mechanism of signaling platform formation in response to elicitor treatment.
Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin
Authors: Vigneron Adrien , Cruaud Perrine , Pignet Patricia , Caprais Jean‐Claude , Gayet Nicolas , Cambon‐Bonavita Marie‐Anne , Godfroy Anne , Toffin Laurent 
Published: November 2013

SummaryThe Sonora Margin cold seeps present on the seafloor a patchiness pattern of white microbial mats surrounded by polychaete and gastropod beds. These surface assemblages are fuelled by abundant organic inputs sedimenting from the water column and upward‐flowing seep fluids. Elevated microbial density was observed in the underlying sediments. A previous study on the same samples identified anaerobic oxidation of methane (AOM) as the potential dominant archaeal process in these Sonora Margin sediments, probably catalysed by three clades of archaeal anaerobic methanotrophs (ANME‐1, ANME‐2 and ANME‐3) associated with bacterial syntrophs. In this study, molecular surveys and microscopic observations investigating the diversity of Bacteria involved in AOM process, as well as the environmental parameters affecting the composition and the morphologies of AOM consortia in the Sonora Margin sediments were carried out. Two groups of Bacteria were identified within the AOM consortia, the Desulfosarcina/Desulfococcus SEEP SRB‐1a group and a Desulfobulbus‐related group. These bacteria showed different niche distributions, association specificities and consortia architectures, depending on sediment surface communities, geochemical parameters and ANME‐associated phylogeny. Therefore, the syntrophic AOM process appears to depend on sulphate‐reducing bacteria with different ecological niches and/or metabolisms, in a biofilm‐like organic matrix.
Functions of the nicotinamide adenine dinucleotide phosphate oxidase family in Ganoderma lucidum: an essential role in ganoderic acid biosynthesis regulation, hyphal branching, fruiting body development, and oxidative‐stress resistance
Authors: Mu Dashuai , Li Chenyang , Zhang Xuchen , Li Xiongbiao , Shi Liang , Ren Ang , Zhao Mingwen 
Published: November 2013

SummaryGanoderma lucidum has drawn worldwide interest with regard to its secondary metabolism and pharmaceutical activity. However, the development of such research has been limited because of a lack of basic biological knowledge. Nicotinamide adenine dinucleotide phosphate oxidases (Nox) have recently been highlighted because of the many important biological roles in plants and animals; however, the exact functions of Nox are still not fully understood in fungi. In this study, we identified two Nox isoforms (NoxA and NoxB) and a regulator, NoxR. RNA interference was used, and silencing of the Nox isoforms and NoxR expression indicated a central role for these genes in hyphal branching, fruiting body development, reactive oxygen species (ROS) generation, ROS resistance and ganoderic acid biosynthesis regulation. Further mechanistic investigation revealed that Nox‐generated ROS elevated cytosolic Ca2+ levels by activating a plasma membrane Ca2+ influx pathway, thereby inducing the Ca2+ signal pathway to regulate ganoderic acid biosynthesis and hyphal branching. Importantly, our results highlight the Nox functions in signal crosstalk between ROS and Ca2+, and these findings provide an excellent opportunity to identify the potential pathway linking ROS networks to calcium signalling in fungi and suggest that plants, animals and fungi share a conserved signal‐crosstalk mechanism.
Phylogenetic constraints on elemental stoichiometry and resource allocation in heterotrophic marine bacteria
Authors: Zimmerman Amy E. , Allison Steven D. , Martiny Adam C. 
Published: November 2013

SummaryThe objective of this study was to evaluate the contribution of evolutionary history to variation in the biomass stoichiometry and underlying biochemical allocation patterns of heterotrophic marine bacteria. We hypothesized that phylogeny significantly constrains biochemical allocation strategy and elemental composition among taxa of heterotrophic marine bacteria. Using a ‘common‐garden’ experimental design, we detected significant interspecific variation in stoichiometry, macromolecule allocation and growth rate among 13 strains of marine Proteobacteria. However, this variation was not well explained by 16S rRNA phylogenetic relationships or differences in growth rate. Heterotrophic bacteria likely experience C‐limitation when consuming resources in Redfield proportions, which consequently decouples growth rate from allocation to rRNA and biomass P content. Accordingly, overall bacterial C : nutrient ratios (C : P = 77, C : N = 4.9) were lower than Redfield proportions, whereas the average N : P ratio of 17 was consistent with the Redfield ratio. Our results suggest that strain‐level diversity is an important driver of variation in the C : N : P ratios of heterotrophic bacterial biomass and that the potential importance of non‐nucleic acid pools of P warrants further investigation. Continued work clarifying the range and controls on the stoichiometry of heterotrophic marine bacteria will help improve understanding and predictions of global ocean C, N and P dynamics.