bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cost‐Effectiveness of Alternative Conservation Strategies with Application to the Pacific Leatherback Turtle
Authors: GJERTSEN HEIDI , SQUIRES DALE , DUTTON PETER H. , EGUCHI TOMOHARU 
Published: January 2014

AbstractAlthough holistic conservation addressing all sources of mortality for endangered species or stocks is the preferred conservation strategy, limited budgets require a criterion to prioritize conservation investments. We compared the cost‐effectiveness of nesting site and at‐sea conservation strategies for Pacific leatherback turtles (Dermochelys coriacea). We sought to determine which conservation strategy or mix of strategies would produce the largest increase in population growth rate per dollar. Alternative strategies included protection of nesters and their eggs at nesting beaches in Indonesia, gear changes, effort restrictions, and caps on turtle takes in the Hawaiian (U.S.A.) longline swordfish fishery, and temporal and area closures in the California (U.S.A.) drift gill net fishery. We used a population model with a biological metric to measure the effects of conservation alternatives. We normalized all effects by cost to prioritize those strategies with the greatest biological effect relative to its economic cost. We used Monte Carlo simulation to address uncertainty in the main variables and to calculate probability distributions for cost‐effectiveness measures. Nesting beach protection was the most cost‐effective means of achieving increases in leatherback populations. This result creates the possibility of noncompensatory bycatch mitigation, where high‐bycatch fisheries invest in protecting nesting beaches. An example of this practice is U.S. processors of longline tuna and California drift gill net fishers that tax themselves to finance low‐cost nesting site protection. Under certain conditions, fisheries interventions, such as technologies that reduce leatherback bycatch without substantially decreasing target species catch, can be cost‐effective. Reducing bycatch in coastal areas where bycatch is high, particularly adjacent to nesting beaches, may be cost‐effective, particularly, if fisheries in the area are small and of little commercial value.Rentabilidad de Estrategias de Conservación Alternativas Aplicadas a Tortugas Laúd del Pacífico
Total carbon and nitrogen in the soils of the world
Authors: Batjes N. H. 
Published: January 2014

SummaryThe soil is important in sequestering atmospheric CO2 and in emitting trace gases (e.g. CO2, CH4 and N2O) that are radiatively active and enhance the ‘greenhouse’ effect. Land use changes and predicted global warming, through their effects on net primary productivity, the plant community and soil conditions, may have important effects on the size of the organic matter pool in the soil and directly affect the atmospheric concentration of these trace gases.A discrepancy of approximately 350 × 1015 g (or Pg) of C in two recent estimates of soil carbon reserves worldwide is evaluated using the geo‐referenced database developed for the World Inventory of Soil Emission Potentials (WISE) project. This database holds 4353 soil profiles distributed globally which are considered to represent the soil units shown on a ½º latitude by ½º longitude version of the corrected and digitized 1 : 5 M FAO–UNESCO Soil Map of the World.Total soil carbon pools for the entire land area of the world, excluding carbon held in the litter layer and charcoal, amounts to 2157–2293 Pg of C in the upper 100 cm. Soil organic carbon is estimated to be 684–724 Pg of C in the upper 30 cm, 1462–1548 Pg of C in the upper 100 cm, and 2376–2456 Pg of C in the upper 200 cm. Although deforestation, changes in land use and predicted climate change can alter the amount of organic carbon held in the superficial soil layers rapidly, this is less so for the soil carbonate carbon. An estimated 695–748 Pg of carbonate‐C is held in the upper 100 cm of the world's soils. Mean C : N ratios of soil organic matter range from 9.9 for arid Yermosols to 25.8 for Histosols. Global amounts of soil nitrogen are estimated to be 133–140 Pg of N for the upper 100 cm. Possible changes in soil organic carbon and nitrogen dynamics caused by increased concentrations of atmospheric CO2 and the predicted associated rise in temperature are discussed.
Progressive damage modelling of 3D fully interlaced woven composite materials
Authors: Koumpias A. S. , Tserpes K. I. , Pantelakis S. 
Published: January 2014

ABSTRACTA progressive damage model (PDM) was developed to simulate the mechanical behaviour and predict strength of 3D fully interlaced woven composite materials. The PDM was applied at the micro‐scale on a homogenised representative volume element (RVE) of the woven material created using the geometry pre‐processor software TexGen. The PDM consists of three modules, namely stress analysis, failure analysis and material property degradation. Stress analysis of the RVE was performed using the finite element method. Failure analysis within the tows was performed using a set of Hashin‐type failure criteria. Material property degradation in the failed elements of the tows was applied using a damage mechanics‐based strain‐softening law. The non‐linear mechanical behaviour of the matrix was simulated using a multi‐linear continuum damage model. The PDM was validated successfully against experimental results from the literature. The mechanical behaviour of the 3D woven composite material was fully characterised by loading the RVE into uniaxial tension and compression in the three axes, and shear in the three planes. The proposed PDM can be used to numerically characterise any type of 3D woven composite material. Furthermore, as the computed mechanical properties of the material are representative at the macro‐scale, they can be used as input to simulation of structural parts made from the specific composite material.
Brugada Syndrome: A Heterogeneous Disease with a Common ECG Phenotype?
Authors: GRAY BELINDA , SEMSARIAN CHRISTOPHER , SY RAYMOND W. 
Published: January 2014

Brugada SyndromeOur understanding of Brugada syndrome (BrS) has evolved since the syndrome was first described in 1992. BrS is considered to be a primary inherited channelopathy often involving the inward sodium current and the diagnosis has traditionally required the exclusion of overt structural heart disease.In view of recently published observations about BrS, we propose that the term BrS may actually encompass a heterogeneous group of disorders with a variety of genetic and clinical phenotypes. This disease has classically been described as a primary electrical disorder involving the sodium channel leading to the characteristic electrocardiogram (ECG) changes of BrS. We challenge the current understanding and propose that patients with structurally normal hearts, family history of sudden cardiac death, with associated genetic abnormalities only account for a subset of patients with the “Brugada pattern” ECG. There may also be some patients with a diagnosis of BrS who may also have features which overlap with arrhythmogenic right ventricular cardiomyopathy. In these patients there may be an underlying structural abnormality. In this context, it is possible that catheter ablation may abolish the “Brugada pattern” ECG changes as well as abolishing the risk of life threatening arrhythmias in these patients.Given the recent developments in the field, we propose a novel comprehensive multimodality model for risk stratification and assessment of patients with BrS. Identification of variations of diseases may facilitate more specific risk stratification models and management paradigms in patients with Brugada ECG pattern.
The perplexing role of autophagy in plant innate immune responses
Authors: Zhou Jie , Yu Jing‐Quan , Chen Zhixiang 
Published: January 2014

SummaryAutophagy is a major intracellular process for the degradation of cytosolic macromolecules and organelles in the lysosomes or vacuoles for the purposes of regulating cellular homeostasis and protein and organelle quality control. In complex metazoan organisms, autophagy is highly engaged during the immune responses through interfaces either directly with intracellular pathogens or indirectly with immune signalling molecules. Studies over the last decade or so have also revealed a number of important ways in which autophagy shapes plant innate immune responses. First, autophagy promotes defence‐associated hypersensitive cell death induced by avirulent or related pathogens, but restricts unnecessary or disease‐associated spread of cell death. This elaborate regulation of plant host cell death by autophagy is critical during plant immune responses to the types of plant pathogens that induce cell death, which include avirulent biotrophic pathogens and necrotrophic pathogens. Second, autophagy modulates defence responses regulated by salicylic acid and jasmonic acid, thereby influencing plant basal resistance to both biotrophic and necrotrophic pathogens. Third, there is an emerging role of autophagy in virus‐induced RNA silencing, either as an antiviral collaborator for targeted degradation of viral RNA silencing suppressors or an accomplice of viral RNA silencing suppressors for targeted degradation of key components of plant cellular RNA silencing machinery. In this review, we summarize this important progress and discuss the potential significance of the perplexing role of autophagy in plant innate immunity.
Evaluation of the AID TB Resistance Line Probe Assay for Rapid Detection of Genetic Alterations Associated with Drug Resistance in Mycobacterium tuberculosis Strains
Authors: Ritter C. , Lucke K. , Sirgel F. A. , Warren R. W. , van Helden P. D. , Böttger E. C. , Bloemberg G. V. 
Published: January 2014

ABSTRACT

The rapid accurate detection of drug resistance mutations in
Mycobacterium tuberculosis
is essential for optimizing the treatment of tuberculosis and limiting the emergence and spread of drug-resistant strains. The TB Resistance line probe assay from Autoimmun Diagnostika GmbH (AID) (Strassburg, Germany) was designed to detect the most prevalent mutations that confer resistance to isoniazid, rifampin, streptomycin, amikacin, capreomycin, fluoroquinolones, and ethambutol. This assay detected resistance mutations in clinical
M. tuberculosis
isolates from areas with low and high levels of endemicity (Switzerland,
n
= 104; South Africa,
n
= 52) and in selected
Mycobacterium bovis
BCG 1721 mutant strains (
n
= 5) with 100% accuracy. Subsequently, the line probe assay was shown to be capable of rapid genetic assessment of drug resistance in MGIT broth cultures, the results of which were in 100% agreement with those of DNA sequencing and phenotypic drug susceptibility testing. Finally, the line probe assay was assessed for direct screening of smear-positive clinical specimens. Screening of 98 clinical specimens demonstrated that the test gave interpretable results for >95% of them. Antibiotic resistance mutations detected in the clinical samples were confirmed by DNA sequencing. We conclude that the AID TB Resistance line probe assay is an accurate tool for the rapid detection of resistance mutations in cultured isolates and in smear-positive clinical specimens.
Rapid Resistome Fingerprinting and Clonal Lineage Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates by Targeted Next-Generation Sequencing
Authors: Arena Fabio , Rolfe P. Alexander , Doran Graeme , Conte Viola , Gruszka Sarah , Clarke Thomas , Adesokan Yemi , Giani Tommaso , Rossolini Gian Maria 
Published: January 2014

ABSTRACT

Thirty-two carbapenem-resistant
Klebsiella pneumoniae
isolates, representative of different resistance mechanisms and clonal lineages, were analyzed with the Pathogenica HAI BioDetection system, based on targeted next-generation sequencing (NGS) technology. With most strains, the system simultaneously yielded comprehensive information on relevant β-lactam resistance determinants and accurate discrimination of clonal lineages, in a shorter time frame and in a less labor-intensive manner than currently available methods for molecular epidemiology analysis. Results supported the usefulness of targeted NGS-based technologies for similar applications.
Superinfection Exclusion in Alphabaculovirus Infections Is Concomitant with Actin Reorganization
Authors: Beperet Inés , Irons Sarah L. , Simón Oihane , King Linda A. , Williams Trevor , Possee Robert D. , López-Ferber Miguel , Caballero Primitivo 
Published: January 2014

ABSTRACTSuperinfection exclusion is the ability of an established virus to interfere with a second virus infection. This effect was studiedin vitroduring lepidopteran-specific nucleopolyhedrovirus (genusAlphabaculovirus, familyBaculoviridae) infection. Homologous interference was detected in Sf9 cells sequentially infected with two genotypes ofAutographa californicamultiple nucleopolyhedrovirus (AcMNPV), each one expressing a different fluorescent protein. This was a progressive process in which a sharp decrease in the signs of infection caused by the second virus was observed, affecting not only the number of coinfected cells observed, but also the level of protein expression due to the second virus infection. Superinfection exclusion was concurrent with reorganization of cytoplasmic actin to F-actin in the nucleus, followed by budded virus production (16 to 20 h postinfection). Disruption of actin filaments by cell treatment with cytochalasin D resulted in a successful second infection. Protection against heterologous nucleopolyhedrovirus infection was also demonstrated, as productive infection of Sf9 cells bySpodoptera frugiperdanucleopolyhedrovirus (SfMNPV) was inhibited by prior infection with AcMNPV, and vice versa. Finally, coinfected cells were observed following inoculation with mixtures of these two phylogenetically distant nucleopolyhedroviruses—AcMNPV and SfMNPV—but at a frequency lower than predicted, suggesting interspecific virus interference during infection or replication. The temporal window of infection is likely necessary to maintain genotypic diversity that favors virus survival but also permits dual infection by heterospecific alphabaculoviruses.IMPORTANCEInfection of a cell by more than one virus particle implies sharing of cell resources. We show that multiple infection, by closely related or distantly related baculoviruses, is possible only during a brief window of time that allows additional virus particles to enter an infected cell over a period of ca. 16 h but then blocks multiple infections as newly generated virus particles begin to leave the infected cell. This temporal window has two important consequences. First, it allows multiple genotypes to almost simultaneously infect cells within the host, thus generating genetically diverse virus particles for transmission. Second, it provides a mechanism by which different viruses replicating in the same cell nucleus can exchange genetic material, so that the progeny viruses may be a mosaic of genes from each of the parental viruses. This opens a completely new avenue of research into the evolution of these insect pathogens.
Insights into the Structure and Assembly of the Bacteriophage ϕ29 Double-Stranded DNA Packaging Motor
Authors: Cao Sheng , Saha Mitul , Zhao Wei , Jardine Paul J. , Zhang Wei , Grimes Shelley , Morais Marc C. 
Published: January 2014

ABSTRACT
The tailed double-stranded DNA (dsDNA) bacteriophage ϕ29 packages its 19.3-kbp genome into a preassembled procapsid structure by using a transiently assembled phage-encoded molecular motor. This process is remarkable considering that compaction of DNA to near-crystalline densities within the confined space of the capsid requires that the packaging motor work against significant entropic, enthalpic, and DNA-bending energies. The motor consists of three phage-encoded components: the dodecameric connector protein gp10, an oligomeric RNA molecule known as the prohead RNA (pRNA), and the homomeric ring ATPase gp16. Although atomic resolution structures of the connector and different pRNA subdomains have been determined, the mechanism of self-assembly and the resulting stoichiometry of the various motor components on the phage capsid have been the subject of considerable controversy. Here a subnanometer asymmetric cryoelectron microscopy (cryo-EM) reconstruction of a connector-pRNA complex at a unique vertex of the procapsid conclusively demonstrates the pentameric symmetry of the pRNA and illuminates the relative arrangement of the connector and the pRNA. Additionally, a combination of biochemical and cryo-EM analyses of motor assembly intermediates suggests a sequence of molecular events that constitute the pathway by which the motor assembles on the head, thereby reconciling conflicting data regarding pRNA assembly and stoichiometry. Taken together, these data provide new insight into the assembly, structure, and mechanism of a complex molecular machine.

IMPORTANCE
Viruses consist of a protein shell, or capsid, that protects and surrounds their genetic material. Thus, genome encapsidation is a fundamental and essential step in the life cycle of any virus. In dsDNA viruses, powerful molecular motors essentially pump the viral DNA into a preformed protein shell. This article describes how a viral dsDNA packaging motor self-assembles on the viral capsid and provides insight into its mechanism of action.
TPCA-1 Is a Direct Dual Inhibitor of STAT3 and NF-κB and Regresses Mutant EGFR-Associated Human Non–Small Cell Lung Cancers
Authors: Nan Jing , Du Yuping , Chen Xing , Bai Qifeng , Wang Yuxin , Zhang Xinxin , Zhu Ning , Zhang Jing , Hou Jianwen , Wang Qin , Yang Jinbo 
Published: January 2014

Abstract
Epidermal growth factor receptor (EGFR) is a clinical therapeutic target to treat a subset of non–small cell lung cancer (NSCLC) harboring EGFR mutants. However, some patients with a similar kind of EGFR mutation show intrinsic resistance to tyrosine kinase inhibitors (TKI). It indicates that other key molecules are involved in the survival of these cancer cells. We showed here that 2-[(aminocarbonyl)amino]-5 -(4-fluorophenyl)-3- thiophenecarboxamide (TPCA-1), a previously reported inhibitor of IκB kinases (IKK), blocked STAT3 recruitment to upstream kinases by docking into SH2 domain of STAT3 and attenuated STAT3 activity induced by cytokines and cytoplasmic tyrosine kinases. TPCA-1 is an effective inhibitor of STAT3 phosphorylation, DNA binding, and transactivation in vivo. It selectively repressed proliferation of NSCLC cells with constitutive STAT3 activation. In addition, using pharmacologic and genetic approaches, we found that both NF-κB and STAT3 could regulate the transcripts of interleukin (IL)-6 and COX-2 in NSCLC harboring EGFR mutations. Moreover, gefitinib treatment only did not efficiently suppress NF-κB and STAT3 activity. In contrast, we found that treatment with TKIs increased phosho-STAT3 level in target cells. Inhibiting EGFR, STAT3, and NF-κB by combination of TKIs with TPCA-1 showed increased sensitivity and enhanced apoptosis induced by gefitinib. Collectively, in this work, we identified TPCA-1 as a direct dual inhibitor for both IKKs and STAT3, whereas treatment targeting EGFR only could not sufficiently repress NF-κB and STAT3 pathways for lung cancers harboring mutant EGFR. Therefore, synergistic treatment of TPCA-1 with TKIs has potential to be a more effective strategy for cancers. Mol Cancer Ther; 13(3); 617–29. ©2014 AACR.
In vitro and in vivo characterisation of the profibrinolytic effect of an inhibitory anti-rat TAFI nanobody
Authors: Hendrickx Maarten L. V. , Zatloukalova Monika , Hassanzadeh-Ghassabeh Gholamreza , Muyldermans Serge , Gils Ann , Declerck Paul J. 
Published: January 2014

SummaryOne of the main disadvantages of current t-PA thrombolytic treatment is the increased bleeding risk. Upon activation, thrombin activatable fibrinolysis inhibitor (TAFI) is a very powerful antifibrinolytic enzyme. Therefore, co-administration of a TAFI inhibitor during thrombolysis could reduce the required t-PA dose without compromising the thrombolytic efficacy. In this study we generated and characterised a nanobody that is inhibitory towards rat TAFI and evaluated its profibrinolytic property in vitro and in vivo. Nanobody VHH-rTAFI-i81 inhibits (at a 16-fold molar ratio nanobody over TAFI) the thrombin/thrombomodulin (T/TM)-mediated activation of rat TAFI (rTAFI) by 83 ± 1.8% with an IC50 of 0.46 (molar ratio nanobody over TAFI). The affinity (KA) of VHH-rTAFI-i81 for rTAFI, as determined by surface plasmon resonance (Biacore®), is 2.5 ± 0.2 × 1010 M−1 and illustrates a very strong binding. In an in vitro clot lysis assay, administration of VHH-rTAFI-i81 strongly enhances the degree of lysis and reduces time to reach full lysis of t-PA-mediated clot lysis. Epitope mapping discloses that Lys392 is of primary importance for the nanobody/rTAFI interaction besides minor contributions of Tyr175 and Glu183. In vivo application of VHH-rTAFI-i81 in a tissue factor-induced mouse thromboembolism model significantly decreases fibrin deposition in the lungs in the absence of exogenous administered t-PA. Nanobody VHH-rTAFI-i81 is a very potent inhibitor of T/TM-mediated TAFI activation. Co-administration of this nanobody and t-PA enhances the fibrinolytic efficacy. In an in vivo mouse thromboembolism model, VHH-rTAFI-i81 reduces fibrin deposition in the lungs.
Modulating Brain Mechanisms Resolving Lexico-semantic Interference during Word Production: A Transcranial Direct Current Stimulation Study
Authors: Henseler Ilona , Mädebach Andreas , Kotz Sonja A. , Jescheniak Jörg D. 
Published: January 2014

AbstractThe aim of the current study was to shed further light on control processes that shape semantic access and selection during speech production. These processes have been linked to differential cortical activation in the left inferior frontal gyrus (IFG) and the left middle temporal gyrus (MTG); however, the particular function of these regions is not yet completely elucidated. We applied transcranial direct current stimulation to the left IFG and the left MTG (or sham stimulation) while participants named pictures in the presence of associatively related, categorically related, or unrelated distractor words. This direct modulation of target regions can help to better delineate the functional role of these regions in lexico-semantic selection. Independent of stimulation, the data show interference (i.e., longer naming latencies) with categorically related distractors and facilitation (i.e., shorter naming latencies) with associatively related distractors. Importantly, stimulation location interacted with the associative effect. Whereas the semantic interference effect did not differ between IFG, MTG, and sham stimulations, the associative facilitation effect was diminished under MTG stimulation. Analyses of latency distributions suggest this pattern to result from a response reversal. Associative facilitation occurred for faster responses, whereas associative interference resulted in slower responses under MTG stimulation. This reduction of the associative facilitation effect under transcranial direct current stimulation may be caused by an unspecific overactivation in the lexicon or by promoting competition among associatively related representations. Taken together, the results suggest that the MTG is especially involved in the processes underlying associative facilitation and that semantic interference and associative facilitation are linked to differential activation in the brain.