bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards a reliability‐based post‐fire assessment method for concrete slabs incorporating information from inspection
Authors: Van Coile Ruben , Caspeele Robby , Taerwe Luc 
Published: January 2014

AbstractAfter a concrete structure has been exposed to fire, a combination of destructive and non‐destructive testing, expert judgment and calculations is used to decide whether the structure should be demolished or repaired, or can continue to be used without repairs or rehabilitation. However, there are many uncertainties associated with both the fire duration and the effect of elevated temperatures on the residual mechanical properties of the materials. Consequently, the maximum service load after fire exposure should be assessed based on reliability considerations in order to provide an adequate level of safety. As this type of calculation is too complex and time‐consuming for practical use, a reliability‐based assessment tool has been developed for concrete structures and applied to slabs to determine the maximum service load after fire. When using the proposed method, a safety level is targeted which is comparable with the safety level associated with the Eurocode format for the design of new structures. It is concluded that the proposed assessment method is both user‐friendly and directly applicable in practice.
Small RNAs in the Vibrionaceae: an ocean still to be explored
Authors: Nguyen An , Jacq Annick 
Published: January 2014

AbstractIn bacteria, the discovery of noncoding small RNAs (sRNAs) as modulators of gene expression in response to environmental signals has brought new insights into bacterial gene regulation, including control of pathogenicity. The Vibrionaceae constitute a family of marine bacteria of which many are responsible for infections affecting not only humans, such as Vibrio cholerae but also fish and marine invertebrates, representing the major cause of mortality in farmed marine species. They are able to colonize many habitats, existing as planktonic forms, in biofilms or associated with various hosts. This high adaptability is linked to their capacity to generate genetic diversity, in part through lateral gene transfer, but also by varying gene expression control. In the recent years, several major studies have illustrated the importance of small regulatory sRNAs in the Vibrionaceae for the control of pathogenicity and adaptation to environment and nutrient sources such as chitin, especially in V. cholerae and Vibrio harveyi. The existence of a complex regulatory network controlled by quorum sensing has been demonstrated in which sRNAs play central roles. This review covers major advances made in the discovery and elucidation of functions of Vibrionaceae sRNAs within the last 10 years.This article is categorized under:

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Preparation and Crystal Structure of Ba4MgF2(CN2)4
Authors: Olivé Corral Anna , Kubus Mariusz , Ströbele Markus , Meyer H.‐Jürgen 
Published: January 2014

AbstractBa4MgF2(CN2)4 was prepared by solid state metathesis reaction from metal fluorides and sodium carbodiimide in a fused copper ampoule at 650 °C. The crystal structure was refined by single‐crystal X‐ray diffraction in the space group P21/c with unit cell dimensions a = 835.1(2) pm, b = 861.7(1) pm, c = 844.2(2) pm, and β = 109.09(2)°. A characteristic feature in the crystal structure of Ba4MgF2(CN2)4 is the two‐dimensional arrangement of infinite [Mg(CN2)4/2(CN2)2] layers along the bc plane of the structure. Barium and fluoride ions are situated in‐between these layers.
Altered proteostasis in aging and heat shock response in C. elegans revealed by analysis of the global and de novo synthesized proteome
Authors: Liang Vanessa , Ullrich Milena , Lam Hong , Chew Yee Lian , Banister Samuel , Song Xiaomin , Zaw Thiri , Kassiou Michael , Götz Jürgen , Nicholas Hannah R. 
Published: January 2014

AbstractProtein misfolding and aggregation as a consequence of impaired protein homeostasis (proteostasis) not only characterizes numerous age-related diseases but also the aging process itself. Functionally related to the aging process are, among others, ribosomal proteins, suggesting an intimate link between proteostasis and aging. We determined by iTRAQ quantitative proteomic analysis inC. eleganshow the proteome changes with age and in response to heat shock. Levels of ribosomal proteins and mitochondrial chaperones were decreased in aged animals, supporting the notion that proteostasis is altered during aging. Mitochondrial enzymes of the tricarboxylic acid cycle and the electron transport chain were also reduced, consistent with an age-associated energy impairment. Moreover, we observed an age-associated decline in the heat shock response. In order to determine how protein synthesis is altered in aging and in response to heat shock, we complemented our global analysis by determining the de novo proteome. For that, we established a novel method that enables both the visualization and identification of de novo synthesized proteins, by incorporating the non-canonical methionine analogue, azidohomoalanine (AHA), into the nascent polypeptides, followed by reacting the azide group of AHA by ‘click chemistry’ with an alkyne-labeled tag. Our analysis of AHA-tagged peptides demonstrated that the decreased abundance of, for example, ribosomal proteins in aged animals is not solely due to degradation but also reflects a relative decrease in their synthesis. Interestingly, although the net rate of protein synthesis is reduced in aged animals, our analyses indicate that the synthesis of certain proteins such as the vitellogenins increases with age.
A phase 1, open-label, dose-escalation study of BIIB022 (anti-IGF-1R monoclonal antibody) in subjects with relapsed or refractory solid tumors
Authors: von Mehren Margaret , Britten Carolyn D. , Pieslor Peter , Saville Wayne , Vassos Artemios , Harris Sarah , Galluppi Gerald R. , Darif Mohamed , Wainberg Zev A. , Cohen Roger B. , Leong Stephen 
Published: January 2014

SummaryPurpose The IGF-1R signaling pathway has been implicated in multiple cancers as important for cell survival, proliferation, invasion and metastasis. BIIB022 is a non-glycosylated human IgG4 monoclonal antibody (mAb) with specificity for IGF-1R. Unlike other anti-IGF1R antibodies, BIIB022 has no effector functions. Additionally, inhibition is via an allosteric rather than competitive mechanism, which further differentiates this antibody from others. We sought to determine the safety and tolerability of BIIB022 and determine the pharmacokinetic (PK) and pharmacodynamic (PD) profile of this antibody. Methods A multi-institutional phase I study evaluated the safety of escalating doses of BIIB022 given IV q3wk until progression or unacceptable toxicity in patients with advanced solid tumors. Five sequential BIIB022 dose cohorts were evaluated using a standard 3 + 3 dose-escalation design (1.5, 5. 10, 20, 30 mg/kg); 10 additional patients were treated at the recommended phase 2 dose. Results 34 patients were treated. Toxicities were manageable and mostly low grade; grade 3–4 hyperglycemia was not observed. No RECIST responses were observed, although three patients had metabolic responses associated with prolonged stable disease. The PK of BIIB022 was nearly linear in the dose range from 10 to 30 mg/kg, with some nonlinearity at lower doses (1.5–5.0 mg/kg), likely due to target-mediated drug disposition of BIIB022 at low serum concentrations. PD analyses showed decrease in IGF-1R levels on leucocytes, with stable serum values of IGF-1 and IGF-2. Conclusions BIIB022 can be safely given at 30 mg/kg IV every 3 weeks with preliminary evidence of biological activity in selected patients.
A hierarchical approach to sustainable agriculture
Authors: Lowrance Richard , Hendrix Paul F. , Odum Eugene P. 
Published: January 2014

Abstract“Sustainable agriculture” means many things to different people in agriculture. At least three different definitions of sustainability are available: sustainability as food sufficiency; sustainability as stewardship; and sustainability as community. Since increased human populations will cause demands for food to continue to grow in the foreseeable future, agricultural sustainability needs to be assessed in ways that will incorporate competing definitions. We suggest that analyzing agriculture as a hierarchical system is the appropriate way to incorporate different concepts of sustainability. Using this concept, we propose a hierarchical definition of sustainability. Agronomic sustainability refers to the ability of a tract of land to maintain productivity over a long period of time. Microeconomic sustainability is dependent on the ability of the farm, as the basic economic unit, to stay in business. Ecological sustainability depends on the maintenance of life-support systems provided by non-agricultural and non-industrial segments of a region. Macroeconomic sustainability is controlled by factors such as fiscal policies and interest rates which determine the viability of national agriculture systems. In our view, there are critical constraints to sustainability at different scales of the agricultural hierarchy. We propose that agronomic constraints are most important at the field scale; microeconomic constraints are dominant at the farm scale; ecological constraints override at the watershed or landscape scale; and macroeconomic constraints are foremost at the regional and national scale. In this paper, we describe the actions of these critical constraints, discuss interactions among various hierarchical levels, and propose ways that agricultural researchers and policy makers can integrate the various views of sustainability.
Explanation in the Social Sciences: Explanation and Understanding in Social Science
Authors: Skorupski John 
Published: January 2014

Hempelian orthodoxy on the nature of explanation in general, and on explanation in the social sciences in particular, holds that(a) full explanations are arguments(b) full explanations must include at least one law(c) reason explanations are causalDavid Ruben disputes (a) and (b) but he does not dispute (c). Nor does he dispute that ‘explanations in both natural and social science need laws in other ways, even when not as part of the explanation itself (p. 97 above). The distance between his view and the covering law theory, he points out, ‘is not as great as it may first appear to be’ (p. 97 above).
A new biofilm-associated colicin with increased efficiency against biofilm bacteria
Authors: Rendueles Olaya , Beloin Christophe , Latour-Lambert Patricia , Ghigo Jean-Marc 
Published: January 2014

Abstract
Formation of bacterial biofilm communities leads to profound physiological modifications and increased physical and metabolic exchanges between bacteria. It was previously shown that bioactive molecules produced within the biofilm environment contribute to bacterial interactions. Here we describe new pore-forming colicin R, specifically produced in biofilms formed by the natural isolate Escherichia coli ROAR029 but that cannot be detected under planktonic culture conditions. We demonstrate that an increased SOS stress response within mature biofilms induces SOS-dependent colicin R expression. We provide evidence that colicin R displays increased activity against E. coli strains that have a reduced lipopolysaccharide length, such as the pathogenic enteroaggregative E. coli LF82 clinical isolate, therefore pointing to lipopolysaccharide size as an important determinant for resistance to colicins. We show that colicin R toxicity toward E. coli LF82 is increased under biofilm conditions compared with planktonic susceptibility and that release of colicin R confers a strong competitive advantage in mixed biofilms by rapidly outcompeting sensitive neighboring bacteria. This work identifies the first biofilm-associated colicin that preferentially targets biofilm bacteria. Furthermore, it indicates that the study of antagonistic molecules produced in biofilm and multispecies contexts could reveal unsuspected, ecologically relevant bacterial interactions influencing population dynamics in natural environments.
Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest
Authors: Mueller Rebecca C , Paula Fabiana S , Mirza Babur S , Rodrigues Jorge L M , Nüsslein Klaus , Bohannan Brendan J M 
Published: January 2014

Abstract
Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.
Plasmonic-cavity model for radiating nano-rod antennas
Authors: Peng Liang , Mortensen N. Asger 
Published: January 2014

AbstractIn this paper, we propose the analytical solution of nano-rod antennas utilizing a cylindrical harmonics expansion. By treating the metallic nano-rods as plasmonic cavities, we derive closed-form expressions for both the internal and the radiated fields, as well as the resonant condition and the radiation efficiency. With our theoretical model, we show that besides the plasmonic resonances, efficient radiation takes advantage of (a) rendering a large value of the rods' radius and (b) a central-fed profile, through which the radiation efficiency can reach up to 70% and even higher in a wide frequency band. Our theoretical expressions and conclusions are general and pave the way for engineering and further optimization of optical antenna systems and their radiation patterns.
Structure–function relationships and supramolecular organization of the EGFR (epidermal growth factor receptor) on the cell surface
Authors: Needham Sarah R. , Zanetti-Domingues Laura C. , Hirsch Michael , Rolfe Daniel J. , Tynan Christopher J. , Roberts Selene K. , Martin-Fernandez Marisa L. , Clarke David T. 
Published: January 2014

Dimerization and higher-order oligomerization are believed to play an important role in the activation of the EGFR (epidermal growth factor receptor). Understanding of the process has been limited by the lack of availability of suitable methods for the measurement in cells of distances in the range 10–100 nm, too short for imaging methods and too long for spectroscopic methods such as FRET. In the present article, we review the current state of our knowledge of EGFR oligomerization, and describe results from a new single-molecule localization method that has allowed the quantitative characterization of the distribution of EGFR–EGFR distances in cells. Recent data suggest the involvement of cortical actin in regulating the formation of EGFR complexes.
Discontinuous leading-strand synthesis: a stop–start story
Authors: Yeeles Joseph T.P. 
Published: January 2014

Reconstitution experiments using replication proteins from a number of different model organisms have firmly established that, in vitro, DNA replication is semi-discontinuous: continuous on the leading strand and discontinuous on the lagging strand. The mechanism by which DNA is replicated in vivo is less clear. In fact, there have been many observations of discontinuous replication in the absence of exogenous DNA-damaging agents. It has also been proposed that replication is discontinuous on the leading strand at least in part because of DNA lesion bypass. Several recent studies have revealed mechanistic details of pathways where replication of the leading strand introduces discontinuities. These mechanisms and their potential contributions to observations of discontinuous replication in vivo will be discussed.
Regulation of IL-6-type cytokine responses by MAPKs
Authors: Costa-Pereira Ana P. 
Published: January 2014

IL-6 (interleukin 6)-type cytokines are pleiotropic molecules, critical for cellular homoeostasis and with well-recognized roles in several human diseases. They all activate JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling and, depending on the particular cytokine, cell type and cellular environment, they can also trigger the activation of MAPK (mitogen-activated protein kinase) and PI3K (phosphoinositide 3-kinase) cascades. Although it is clear that JAK/STAT and MAPK reciprocally regulate each other, how these signalling pathways are fully integrated remains to be fully understood. Not only do cells have to be able to integrate and conciliate what are often contradictory signalling cues, but they are also subject to complex regulatory mechanisms involving these pathways. More specifically, we have shown recently that ERK2 (extracellular-signal-regulated kinase 2) is required for the transcriptional regulation of gp130 (glycoprotein 130), a key receptor complex component for most IL-6-type cytokines. ERK2 not only binds to the gp130 promoter and is required for full expression of the protein, but it also regulates the stability of gp130 mRNA. This function of ERK2 is not shared by ERK1 and it probably represents an entirely novel function for this prominent kinase.
Probing large conformational rearrangements in wild-type and mutant spectrin using structural mass spectrometry
Authors: Sriswasdi Sira , Harper Sandra L. , Tang Hsin-Yao , Gallagher Patrick G. , Speicher David W. 
Published: January 2014

Significance
Chemical cross-linking coupled with mass spectrometry has recently emerged as a powerful method for providing medium-resolution spatial information for proteins that are too large or too flexible for crystallography or NMR. To date, crystal structures of only small segments of the highly flexible, conformationally dynamic spectrin family of proteins have been obtained. In this study we combined cross-link–derived spatial constraints with homology modeling to produce the first experimentally verified medium-resolution structures of wild-type spectrin closed dimers and tetramers. These structures coupled with the closed dimer structure of a very common spectrin mutation associated with hereditary hemolytic anemia provide mechanistic insights into how some mutations located large distances from the spectrin tetramerization site can destabilize red cell membranes.
Sel1L is indispensable for mammalian endoplasmic reticulum-associated degradation, endoplasmic reticulum homeostasis, and survival
Authors: Sun Shengyi , Shi Guojun , Han Xuemei , Francisco Adam B. , Ji Yewei , Mendonça Nuno , Liu Xiaojing , Locasale Jason W. , Simpson Kenneth W. , Duhamel Gerald E. , Kersten Sander , Yates John R. , Long Qiaoming , Qi Ling 
Published: January 2014

Significance
This study provides insights into the physiological role of Sel1L, an adaptor protein for the ubiquitin ligase Hrd1 in endoplasmic reticulum-associated degradation (ERAD). Using both animal and cell models, this study provides unequivocal evidence for an indispensable role of Sel1L in Hrd1 stabilization, mammalian ERAD, endoplasmic reticulum homeostasis, protein translation, and cellular and organismal survival. Moreover, generation of inducible knockout mouse and cell models deficient in both Sel1L and Hrd1 provides an unprecedented opportunity to elucidate the functional importance of this key branch of ERAD in vivo and to identify its physiological substrates.
Comparing Ultrasonography and Endoscopy for Early Gender Identification of Juvenile Siberian Sturgeon
Authors: Munhofen Jennifer L , Jiménez David A , Peterson Doug L , Camus Alvin C , Divers Stephen J 
Published: January 2014

Abstract
Early gender identification is economically advantageous in sturgeon aquaculture to facilitate the targeting of food and spatial resources to females for caviar production. In addition, many species of free-ranging sturgeon are threatened or critically endangered, and the ability to identify gender and evaluate gonads can reveal pertinent biological information that can lead to better management and recovery plans. We compared the speed and accuracy of ultrasonography and endoscopy in identifying gender in 143 juvenile Siberian Sturgeon Acipenser baeri using gonadal histology as the gold standard. The age-3 and age-4 sturgeon were anesthetized with buffered tricaine methanesulfonate and evaluated using ultrasonography and endoscopy; endoscopic gonadal biopsy was then done for histologic confirmation. All fish recovered normally, and there was no postprocedural morbidity or mortality. Histology confirmed the gender for 128 of the 140 (91.4%) fish. Histology and endoscopy agreed on the gender of 124 of the 128 (96.9%) fish, while histology and ultrasonography agreed on 113 of the 128 (88.3%) fish. Ultrasonography (mean time, 11.2 s) was significantly faster than endoscopy (22.3 s), while endoscopy was more accurate but more invasive. Diagnostic accuracy, speed, and invasiveness are factors to consider when selecting a method of gender identification for commercial and free-ranging populations.
Relation between Nucleic Acid Indices and Growth Rate in Fed and Fasting Juvenile Scup
Authors: Mercaldo-Allen Renee , Kuropat Catherine A , Perry Dean M , Redman Dylan H 
Published: January 2014

Abstract
The relationship between nucleic acid indices and daily instantaneous growth rate was determined for juvenile Scup Stenotomus chrysops in the laboratory. Weight-based growth of Scup was measured for three 1-week intervals during a 6-week feeding experiment and showed a significant positive correlation with both RNA concentration (RNA; μg/mg tissue wet weight) and DNA concentration (DNA; μg/mg tissue wet weight), while the RNA: DNA ratio was not significantly correlated with the weight- or length-based growth rate. The concentration of DNA showed a significant negative correlation with length-based growth rate. Mean fish weight increased from 1.022 to 10.404 g, and mean TL increased from 43.219 to 85.377 mm. Changes in nucleic acid indices were measured in fish that were deprived of food over a 9-d period. The RNA and RNA: DNA ratio values declined significantly within 5 d after fasting began, while DNA remained relatively stable. This study provides baseline nucleic acid values for fed and starved juvenile Scup over a range of fish sizes.