bluuebunny/crossref_metadata_2025_split huggingface dataset:
First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis)
Authors: Ristau Kai , Steinfartz Sebastian , Traunspurger Walter 
Published: August 2013

AbstractFree‐living nematodes are ubiquitous and highly abundant in terrestrial and aquatic environments, where they sustain ecosystem functioning by mineralization processes and nutrient cycling. Nevertheless, very little is known about their true diversity and intraspecific population structure. Recent molecular studies on marine nematodes indicated cryptic diversity and strong genetic differentiation of distinct populations, but for freshwater nematode species, analogous studies are lacking. Here, we present the first extensive molecular study exploring cryptic species diversity and genetic population structure of a widespread freshwater nematode morphospecies, Tobrilus gracilis, from nine postglacially formed European lakes. Taxonomic species status of individuals, analysed for fragments of the mitochondrial COI gene and for the large (LSU) and small (SSU) ribosomal subunits, were determined by morphological characteristics. Mitochondrial and nuclear markers strongly supported the existence of three distinct genetic lineages (Tg I–III) within Tobrilus gracilis, suggesting that this morphospecies indeed represents a complex of highly differentiated biological species. High genetic diversity was also observed at the population level. Across the nine lakes, 19 mitochondrial, and seven (LSU) and four (SSU) nuclear haplotypes were determined. A phylogeographical analysis revealed remarkable genetic differentiation even among neighbouring lake populations for one cryptic lineage. Priority and persistent founder effects are possible explanations for the observed population structure in the postglacially colonized lakes, but ask for future studies providing direct estimates of freshwater nematode dispersal rates. Our study suggests therefore that overall diversity of limnetic nematodes has been so far drastically underestimated and challenges the assumed ubiquitous distribution of other, single freshwater nematode morphospecies.
High connectivity across the fragmented chemosynthetic ecosystems of the deepAtlanticEquatorialBelt: efficient dispersal mechanisms or questionable endemism?
Authors: Teixeira Sara , Olu Karine , Decker Carole , Cunha Regina L. , Fuchs Sandra , Hourdez Stéphane , Serrão Ester A. , Arnaud‐Haond Sophie 
Published: August 2013

AbstractChemosynthetic ecosystems are distributed worldwide in fragmented habitats harbouring seemingly highly specialized communities. Yet, shared taxa have been reported from highly distant chemosynthetic communities. These habitats are distributed in distinct biogeographical regions, one of these being the so‐calledAtlanticEquatorialBelt (AEB). Here, we combined genetic data (COI) from several taxa to assess the possible existence of cryptic or synonymous species and to detect the possible occurrence of contemporary gene flow among populations of chemosynthetic species located on both sides of theAtlantic. SeveralEvolutionarySignificantUnits (ESUs) of Alvinocarididae shrimp andVesicomyidae bivalves were found to be shared across seeps of theAEB. Some were also common to hydrothermal vent communities of theMid‐AtlanticRidge (MAR), encompassing taxa morphologically described as distinct species or even genera. The hypothesis of current or very recent large‐scale gene flow among seeps and vents was supported by microsatellite analysis of the shrimp speciesAlvinocaris muricola/Alvinocaris markensisacross theAEBandMAR. Two nonmutually exclusive hypotheses may explain these findings. The dispersion of larvae or adults following strong deep‐sea currents, possibly combined with biochemical cues influencing the duration of larval development and timing of metamorphosis, may result in large‐scale effective migration among distant spots scattered on the oceanic seafloor. Alternatively, these results may arise from the prevailing lack of knowledge on the ocean seabed, apart from emblematic ecosystems (chemosynthetic ecosystems, coral reefs or seamounts), where the widespread classification of endemism associated with many chemosynthetic taxa might hide wider distributions in overlooked parts of the deep sea.
Dynamic Planning of Facility Locations with Benefits from Multitype Facility Colocation
Authors: Xie Weijun , Ouyang Yanfeng 
Published: August 2013

AbstractThis article presents a mixed‐integer programming model for a multitype facility colocation problem with capacity expansion over a multiperiod horizon. This problem is motivated by the emerging U.S. biofuel industry that is rapidly expanding its infrastructure facilities to produce bioethanol from agricultural crops. Each type of facility (e.g., corn‐ or cellulose‐based biorefinery) requires a different type of raw material (e.g., corn or perennial grass), but they produce the same final product (e.g., bioethanol), and colocation of multiple types of facilities results in cost‐saving benefits due to complementary production process and byproduct recycling. Multiple solution approaches (i.e., Lagrangian relaxation, Benders decomposition, and accelerated Benders decomposition) are proposed to solve this problem. Numerical experiments show that accelerated Benders decomposition most effectively solves large‐sized problems in a short amount of time. Various managerial insights are also drawn from the computational results.
MATHEMATICAL STUDY OF A PEST CONTROL MODEL INCORPORATING STERILE INSECT TECHNIQUE
Authors: BHATTACHARYYA R. , MUKHOPADHYAY B. 
Published: August 2013

AbstractThe menace of insect pests is a topic of major concern throughout the world. Chemical pesticides are conventionally used to control these insect pests. However, the adverse effects of these synthetic pesticides, such as high toxicity from residues in food, contamination of water and the environment resulting in human health hazard and resistance of the pest to the pesticides have necessitated development of some nonconventional approaches of biological pest control.In this research, we have focused on a mathematical model of biological pest control using the sterile insect release technique. Unlike most of the existing modeling studies in this field that mainly deal with the pest population only, we have incorporated the crop population as a distinct dynamical equation together with the fertile and sterile insect pests. Local stability analysis is performed around the crop and fertile insect free axial equilibrium, the fertile‐insect‐free boundary equilibrium, the crop‐free boundary equilibrium and the equilibrium point of coexistence. From the study we have derived a number of thresholds for the SIRR (the main parameter for our study) that cause existence and or extinction of the crop population as well as the fertile insect pests. A global study of the model system using comparison arguments revealed existence of a global attractor for the system. Numerical simulations are done to support and augment analytical results.
THE DYNAMICS OF AN ANIMAL—VEGETATION SYSTEM: SHEEP FARMING
Authors: DA ROCHA JOSÉ‐MARÍA , SKONHOFT ANDERS 
Published: August 2013

AbstractThe paper studies the economy and ecology of sheep farming at the farm level in a Nordic context, with a crucial distinction between the outdoors grazing season and the winter indoors feeding season, and where climate conditions fix the length of the grazing season. Two different categories of animals, ewes (adult females) and lambs, and one plant species are included in our ecological model. The farmer is assumed to maximize present‐value profit where the revenue is made up income from meat and wool production. We find that livestock cycles may represent an optimal management policy. We also show that in a possible steady state with a constant number of animals and constant vegetation quantity, slaughtering either only lambs or only ewes is optimal.
An Efficacy Analysis of Surgical Timing and Procedures for High‐Energy Complex Tibial Plateau Fractures
Authors: Xu Yun‐qin , Li Qiang , Shen Tu‐gang , Su Pei‐hua , Zhu Ya‐zhong 
Published: August 2013

ObjectiveTo identify the most effective treatment for application to high‐energy complex plateau fractures.Methods125 patients with closed high‐energy complex tibial plateau fractures who had been surgically treated between 2003 and 2010 were reviewed retrospectively. Five procedure methods were studied (e.g. four open reduction and internal fixations, and close reduction via a minimal incision with hybrid external fixation) in five surgical timings, with a control group. The incidence of wound complications after operative treatment in the five surgical timings and the clinical effects of the five surgical procedure options were evaluated statistically. A postoperative follow‐up ranging 26–110 months (mean, 36.5 months) was performed.ResultsAmong the various groups, the respective overall wound complication incidences were 20.0%, 41.6%, 33.3%, 2.5%, and 16.7% within 4 hours, 4 hours to 3 days, 3–5 days, 5–8 days, and more than 8 days after injury. Failed fixation was clearly observed in Group 1 (23.1%, 6/26) and Group 5 (21.7%, 5/23) (P < 0.05). Significant differences were also found among Group 2 (92.6%), Group 3 (93.3%), and Group 5 (69.6%), in terms of the good and excellent rate of joint function according to the Rasmussen score (P < 0.05).ConclusionThe optimal surgical timing is within 4 hours after trauma, for which no obvious swelling was observed in the limbs. This is followed by surgical timing within 5–8 days, after which trauma showed only subsided limb swelling. Dual plating provides the best stabilization option, as it allows early joint mobilization, cartilage regeneration, and joint remodeling, thus decreasing the risk of joint stiffness. Hybrid external fixation may provide relative stability to maintain fracture alignment without the need for massive soft tissue dissection, and also minimizes blood loss and potential soft tissue complications.
Re‐conceptualising Prenatal Life Stressors in Predicting Post‐partum Depression: Cumulative‐, Specific‐, and Domain‐specific Approaches to Calculating Risk
Authors: Liu Cindy H. , Tronick Ed 
Published: August 2013

AbstractBackgroundPrenatal life stress predicts post‐partum depression (PPD); however, studies generally examine individual stressors (a specific approach) or the summation of such exposure (a cumulative approach) and their associations with PPD. Such approaches may oversimplify prenatal life stress as a risk factor for PPD. We evaluated approaches in assessing prenatal life stress as a predictor of PPD diagnosis, including a domain‐specific approach that captures cumulative life stress while accounting for stress across different life stress domains: financial, relational, and physical health.MethodsThe Pregnancy Risk Assessment Monitoring System, a population‐based survey, was used to analyse the association of prenatal life stressors with PPD diagnoses among 3566 New York City post‐partum women.ResultsSpecific stressors were not associated with PPD diagnosis after controlling for sociodemographic variables. Exposure to a greater number of stressors was associated with PPD diagnosis, even after adjusting for both sociodemographic variables and specific stressors [odds ratio (OR) = 3.1, 95% confidence interval (CI) = 1.5, 6.7]. Individuals reporting a moderate‐to‐high number of financial problems along with a moderate‐to‐high number of physical problems were at greater odds of PPD (OR = 4.2, 95% CI = 1.2, 15.3); those with a moderate‐to‐high number of problems in all three domains were at over fivefold increased odds of PPD (OR = 5.5, CI = 1.1, 28.5).ConclusionsIn assessing prenatal stress, clinicians should consider the extent to which stressors occur across different life domains; this association appears stronger with PPD diagnosis than simple assessments of individual stressors, which typically overestimate risk or cumulative exposures.
Role of the epithelial cell rests of Malassez in the development, maintenance and regeneration of periodontal ligament tissues
Authors: Xiong Jimin , Gronthos Stan , Bartold P. Mark 
Published: August 2013

AbstractPeriodontitis is a highly prevalent inflammatory disease that results in damage to the tooth‐supporting tissues, potentially leading to tooth loss. Periodontal tissue regeneration is a complex process that involves the collaboration of two hard tissues (cementum and alveolar bone) and two soft tissues (gingiva and periodontal ligament). To date, no periodontal‐regenerative procedures provide predictable clinical outcomes. To understand the rational basis of regenerative procedures, a better understanding of the events associated with the formation of periodontal components will help to establish reliable strategies for clinical practice. An important aspect of this is the role of the Hertwig's epithelial root sheath in periodontal development and that of its descendants, the epithelial cell rests of Malassez, in the maintenance of the periodontium. An important structure during tooth root development, the Hertwig's epithelial root sheath is not only a barrier between the dental follicle and dental papilla cells but is also involved in determining the shape, size and number of roots and in the development of dentin and cementum, and may act as a source of mesenchymal progenitor cells for cementoblasts. In adulthood, the epithelial cell rests of Malassez are the only odontogenic epithelial population in the periodontal ligament. Although there is no general agreement on the functions of the epithelial cell rests of Malassez, accumulating evidence suggests that the putative roles of the epithelial cell rests of Malassez in adult periodontal ligament include maintaining periodontal ligament homeostasis to prevent ankylosis and maintain periodontal ligament space, to prevent root resorption, to serve as a target during periodontal ligament innervation and to contribute to cementum repair. Recently, ovine epithelial cell rests of Malassez cells have been shown to harbor clonogenic epithelial stem‐cell populations that demonstrate similar properties to mesenchymal stromal/stem cells, both functionally and phenotypically. Therefore, the epithelial cell rests of Malassez, rather than being ‘cell rests’, as indicated by their name, are an important source of stem cells that might play a pivotal role in periodontal regeneration.
Neutrophil extracellular traps as a new paradigm in innate immunity: friend or foe?
Authors: Cooper Paul R. , Palmer Lisa J. , Chapple Iain L. C. 
Published: August 2013

AbstractThe discovery of neutrophil extracellular traps in 2004 opened a fascinating new chapter in immune‐mediated microbial killing. Brinkman et al. demonstrated that neutrophils, when catastrophically stimulated, undergo a novel form of programmed cell death (neutrophil extracellular trap formation) whereby they decondense their entire nuclear chromatin/DNA and release the resulting structure into the cytoplasm to mix with granule‐derived antimicrobial peptides before extruding these web‐like structures into the extracellular environment. The process requires the activation of the granule enzyme peptidyl arginine deiminase‐4, the formation of reactive oxygen species (in particular hypochlorous acid), the neutrophil microtubular system and the actin cytoskeleton. Recent work by Yousefi et al. demonstrated that exposure to different agents for shorter stimulation periods resulted in neutrophil extracellular trap release from viable granulocytes, and that such neutrophil extracellular traps comprised mitochondrial DNA rather than nuclear DNA and were also capable of microbial entrapment and destruction. Deficiency in NADPH‐oxidase production (as found in patients with chronic granulomatous disease) results in an inability to produce neutrophil extracellular traps and, along with their failure to produce antimicrobial reactive oxygen species, these patients suffer from severe, and sometimes life‐threatening, infections. However, conversely the release of nuclear chromatin into tissues is also potentially autoimmunogenic and is now associated with the generation of anti‐citrullinated protein antibodies in seropositive rheumatoid arthritis. Other neutrophil‐derived nuclear and cytoplasmic contents are also pathogenic, either through direct effects on tissues or via autoimmune processes (e.g. autoimmune vasculitis). In this review, we discuss the plant origins of a highly conserved innate immune method of microbial killing, the history and biology of neutrophil extracellular traps and their role in defence and in human diseases. We attempt to resolve areas of controversy and propose roles for excess neutrophil extracellular trap release from hyperactive/reactive neutrophils and for the unique peptidyl arginine deiminase enzyme of Porphyromonas gingivalis in the pathogenesis of periodontitis, and subsequently a role for periodontitis/the peptidyl arginine deiminase enzyme of P. gingivalis in the causal pathway of autoimmune diseases such as rheumatoid arthritis. We propose that neutrophil extracellular trap and peptidyl arginine deiminase release may propagate tissue‐destructive mechanisms rather than provide protection in susceptible individuals and that release of host‐derived DNase may play an important role in the digestion and removal of neutrophil extracellular traps within tissues.
Defensins and LL‐37: a review of function in the gingival epithelium
Authors: Greer Ara , Zenobia Camille , Darveau Richard P. 
Published: August 2013

AbstractAntimicrobial peptides represent an important aspect of the innate defense system that contributes to the control of bacterial colonization and infection. As studies have progressed it has become clear that antimicrobial peptides manifest other functions in addition to their antimicrobial effects. These functions include chemotaxis of numerous types of host cells involved in both the innate and adaptive immune responses. In this review, the antimicrobial activity, the regulation and the contribution to host homeostasis of alpha‐defensins and LL‐37, as well as of beta‐defensins, are discussed in the context of their specific tissue locations in the junctional epithelium and oral epithelium, respectively.
Macrophage subsets and osteoimmunology: tuning of the immunological recognition and effector systems that maintain alveolar bone
Authors: Sima Corneliu , Glogauer Michael 
Published: August 2013

AbstractChronic and aggressive periodontal diseases are characterized by the failure to resolve local inflammation against periodontopathogenic bacteria in the subgingival biofilm. Alveolar bone resorption is associated with altered innate and adaptive immune responses to periodontal pathogens. Macrophage‐derived cytokines, chemokines and growth factors, present in both destructive and reparative phases of periodontitis, are elevated in numerous animal and human studies. Macrophage polarization to either a predominantly pro‐inflammatory or anti‐inflammatory phenotype may be a critical target for monitoring disease activity, modulating immune responses to subgingival biofilms in patients at risk and reducing alveolar bone loss.
Effect of Different Levels of Glycerol and Cholesterol‐Loaded Cyclodextrin on Cryosurvival of Ram Spermatozoa
Authors: Motamedi‐Mojdehi R , Roostaei‐Ali Mehr M , Rajabi‐Toustani R 
Published: August 2013

ContentsThis study was conducted to determine the optimum level of glycerol and cholesterol‐loaded cyclodextrin (CLC) in a Tris‐based diluent for cryopreservation of ram spermatozoa.Ram semen was treated with 0, 1.5, 3 or 4.5 mgCLC/120 × 106 cells inTris‐based diluents containing 3, 5 or 7% glycerol in a factorial arrangement 3 × 4 and frozen in liquid nitrogen vapour. Sperm motility, viability (eosin–nigrosin staining) and functional membrane integrity (hypo‐osmotic swelling test) were assessed immediately after thawing (0 h) and subsequently after 3 and 6 h at 37°C. There was an interaction betweenCLCand glycerol on the functional membrane integrity (p < 0.05). In the presence of 3% glycerol, the highest functional membrane integrity (32.2%) was found in the spermatozoa treated with 1.5 mgCLC/120 × 106 sperm. Post‐thaw sperm motility was highest in 1.5 mgCLCimmediately after thawing (40.5%) and after 3‐h (30.6%) incubation at 37°C (p < 0.05). Viability of spermatozoa was higher in allCLCtreatments than in the untreated samples, and it was highest (33.9%) in the spermatozoa treated with 1.5 mgCLC(p < 0.05). These data indicate that the addition of cholesterol to sperm membranes by 1.5 mgCLC/120 × 106 cells may allow the use of a lower concentration of glycerol (3%), which is sufficient to mitigate the detrimental effects of freezing and thawing.
Multiple-Membership Multiple-Classification Models for Social Network and Group Dependences
Authors: Tranmer Mark , Steel David , Browne William J. 
Published: August 2013

SummaryThe social network literature on network dependences has largely ignored other sources of dependence, such as the school that a student attends, or the area in which an individual lives. The multilevel modelling literature on school and area dependences has, in turn, largely ignored social networks. To bridge this divide, a multiple-membership multiple-classification modelling approach for jointly investigating social network and group dependences is presented. This allows social network and group dependences on individual responses to be investigated and compared. The approach is used to analyse a subsample of the Adolescent Health Study data set from the USA, where the response variable of interest is individual level educational attainment, and the three individual level covariates are sex, ethnic group and age. Individual, network, school and area dependences are accounted for in the analysis. The network dependences can be accounted for by including the network as a classification in the model, using various network configurations, such as ego-nets and cliques. The results suggest that ignoring the network affects the estimates of variation for the classifications that are included in the random part of the model (school, area and individual), as well as having some influence on the point estimates and standard errors of the estimates of regression coefficients for covariates in the fixed part of the model. From a substantive perspective, this approach provides a flexible and practical way of investigating variation in an individual level response due to social network dependences, and estimating the share of variation of an individual response for network, school and area classifications.
Large Covariance Estimation by Thresholding Principal Orthogonal Complements
Authors: Fan Jianqing , Liao Yuan , Mincheva Martina 
Published: August 2013

SummaryThe paper deals with the estimation of a high dimensional covariance with a conditional sparsity structure and fast diverging eigenvalues. By assuming a sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross-sectional correlation even after taking out common but unobservable factors. We introduce the principal orthogonal complement thresholding method ‘POET’ to explore such an approximate factor structure with sparsity. The POET-estimator includes the sample covariance matrix, the factor-based covariance matrix, the thresholding estimator and the adaptive thresholding estimator as specific examples. We provide mathematical insights when the factor analysis is approximately the same as the principal component analysis for high dimensional data. The rates of convergence of the sparse residual covariance matrix and the conditional sparse covariance matrix are studied under various norms. It is shown that the effect of estimating the unknown factors vanishes as the dimensionality increases. The uniform rates of convergence for the unobserved factors and their factor loadings are derived. The asymptotic results are also verified by extensive simulation studies. Finally, a real data application on portfolio allocation is presented.