bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three‐dimensional effects in finite thickness plates weakened by rounded notches and holes under in‐plane shear
Authors: Berto F. , Marangon C. 
Published: August 2013

ABSTRACTIt is well known that in cracked plates under in‐plane shear loading, an induced out‐of‐plane mode, due to the Poisson's effect, is automatically generated. Some recent studies have shown the importance of this coupled mode (called mode O) in plates weakened by sharp V‐notches characterized by different notch opening angles. Particular attention has been paid to the scale effect focusing also on the implications of the coupled mode to different material scale levels.Also when the notch root radius is different from zero, the out‐of‐plane mode continues to exist, and its intensity with respect to the generating mode depends on the notch radius and the plate thickness. Aim of this paper is to discuss the main features of the out‐of‐plane mode dealing with three‐dimensional plates weakened by blunt notches. In particular, some results from blunt V‐notches, circular and elliptic holes are discussed in detail and presented here. The main key‐point highlighted in the present contribution is that always three‐dimensional effects exist in finite thickness plates, because mode I, II and III cannot exist in isolation. The importance of induced modes varies from case to case and depends on the geometry of the component and on the externally applied load. These effects cannot be neglected a priori even if, in some cases, they may be negligible.
Reappraising the effects of habitat structure on river macroinvertebrates
Authors: Barnes Jacqueline B. , Vaughan Ian P. , Ormerod Steve J. 
Published: August 2013

Summary

Although rivers are highly structured physically, generalisations about the consequences for macroinvertebrates remain elusive. In part, this reflects the difficulty of quantifying structure per se as well as differentiating the effects on organisms of complexity (i.e. the total abundance of structural features), heterogeneity (i.e. the composition and spatial arrangement of different structural features) and surface area.

Three hypotheses about habitat structure were tested at the patch scale (<0.1 m2) in tributaries of the Rivers Wye and Usk, mid‐Wales (U.K.): (i) greater habitat heterogeneity and surface complexity alter macroinvertebrate assemblage composition and increase diversity, richness and abundance, (ii) the effects of complexity on macroinvertebrates are distinct from those of increased surface area, and (iii) habitat structure (heterogeneity and complexity) is a major determinant of variations in macroinvertebrates among habitat types (bedrock, silt, sand, gravel, pebbles and cobbles).

Surface complexity, described using fractal dimension, and surface area were estimated from ten riverbed profiles at 0.25 × 0.25 m locations sampled for macroinvertebrates. Habitat heterogeneity was determined within 1 m radii and described by principal components reflecting the patchiness of habitat mosaics (PC1) and the evenness of patch sizes (PC2). Relationships between these heterogeneity PCs, fractal dimension, surface area, habitat type and macroinvertebrates were analysed using models excluding and including habitat type. We also used hierarchical partitioning to investigate the variance explained independently and jointly by each of the variables.

Bedrock was the least complex habitat, whilst pebbles were the most complex. Habitat mosaics surrounding cobbles had the most variable patch sizes, whilst those around gravel or bedrock were the most even.

Complexity (but not heterogeneity) increased macroinvertebrate diversity and abundance independently of surface area, but independently accounted for <5% of the variation in macroinvertebrates. Complexity and surface area also independently increased taxonomic richness, but rarefaction showed that this was an artefact of increased abundances. Habitat type explained more of the variation (up to 21%) and rendered complexity and surface area redundant in our models. Bedrock, silt and sand typically had reduced diversity, richness and abundance of (mostly) Ephemeroptera, Plecoptera and Trichoptera, whilst silt had abundant Chironomidae.

These results support the first two hypotheses, but only in part. Habitat heterogeneity did not affect macroinvertebrates, whilst the effects of complexity were weak. The major implication is that habitat type affects macroinvertebrates through factors other than structure alone, and we advocate a wider reappraisal of the processes involved.
The role of SDF‐1 and CXCR4 on odontoblastic differentiation in human dental pulp cells
Authors: Kim D. S. , Kim Y. S. , Bae W. J. , Lee H. J. , Chang S. W. , Kim W. S. , Kim E. C. 
Published: August 2013

AbstractAimTo examine the role of stromal cell–derived factor 1 (SDF‐1) signalling during odontogenic differentiation in human dental pulp cells (HDPCs).MethodologyHuman dental pulp cells were treated with differentiation medium, recombinant human SDF‐1, neutralizing antibody for SDF‐1 or CXCR4, pertussis toxin (PTX) and AMD3100. The expression of SDF‐1 and its receptor chemokine receptor type 4 (CXCR4) was measured by reverse transcription–polymerase chain reaction (RT‐PCR) and Western blotting. Odontoblastic differentiation was determined using alkaline phosphatase (ALP) activity assay, mineralized nodule formation and marker mRNAs by RT‐PCR.ResultsMarked upregulation of SDF‐1 and CXCR4 mRNA and protein was observed in cells grown 7 days in osteogenic induction medium. The addition of recombinant human SDF‐1 to HDPCs significantly (P < 0.05) increased ALP activity, mineralized nodule formation and odontoblast marker mRNAs in a dose‐dependent manner. Blocking SDF‐1 signalling using antibodies against SDF‐1 or CXCR4, or the G‐protein‐coupled receptor inhibitor PTX, and CXCR4 inhibitor AMD3100, strongly suppressed induction of odontogenic differentiation in HDPCs.ConclusionsOdontoblastic differentiation was stimulated by SDF‐1 activation and repressed by SDF‐1/CXCR4 inhibition. Thus, SDF‐1/CXCR4 signalling may be a new therapeutic target and strategy to promote repair and regeneration in endodontics.
Role of regulatory T cells during virus infection
Authors: Veiga‐Parga Tamara , Sehrawat Sharvan , Rouse Barry T. 
Published: August 2013

SummaryThe host response to viruses includes multiple cell types that have regulatory function. Most information focuses on CD4+ regulatory T cells that express the transcription factor Foxp3+ (Tregs), which are the topic of this review. We explain how viruses through specific and non‐specific means can trigger the response of thymus‐derived natural Tregs as well as induce Tregs. The latter derive under appropriate stimulation conditions either from uncommitted precursors or from differentiated cells that convert to become Tregs. We describe instances where Tregs appear to limit the efficacy of antiviral protective immunity and other, perhaps more common, immune‐mediated inflammatory conditions, where the Tregs function to limit the extent of tissue damage that occurs during a virus infection. We discuss the controversial roles that Tregs may play in the pathogenesis of human immunodeficiency and hepatitis C virus infections. The issue of plasticity is discussed, as this may result in Tregs losing their protective function when present in inflammatory environments. Finally, we mention approaches used to manipulate Treg numbers and function and assess their current value and likely future success to manage the outcome of virus infection, especially those that are responsible for chronic tissue damage.
The contextual role of TNFR family members in CD8+ T‐cell control of viral infections
Authors: Wortzman Michael E. , Clouthier Derek L. , McPherson Ann J. , Lin Gloria H. Y. , Watts Tania H. 
Published: August 2013

SummaryImmunity to viruses must be tightly controlled to avoid pathology. Receptors and ligands of the tumor necrosis factor (TNF) family play important roles in controlling lymphocyte activation and survival during an immune response. The role of specific TNF receptor (TNFR) family members in antiviral immunity depends on the stage of the immune response and can vary with the virus type and its virulence. Here, we focus on five members of the TNFR family that are prominently expressed on CD8+ T cells during viral infections, namely, 4‐1BB (CD137), CD27, OX40 (CD134), GITR, and TNFR2. 4‐1BB, CD27, OX40, and GITR have primarily prosurvival roles for CD8+ T cells during viral infection, although under some circumstances 4‐1BB, GITR, or CD27 signals can limit immunity. Although TNFR2 can be costimulatory under some circumstances, its main role in CD8+ T‐cell responses during viral infection appears to be in contraction of the response. Several TNF family ligands are being explored as adjuvants for viral vaccines, and agonistic antibodies to TNFR family members are being investigated for immunotherapy of chronic viral infection alone and in combination with checkpoint blockade. Such therapies will require thorough and specific optimization to avoid pathology induced by hyperstimulation of these pathways.
The expanding role of NLRs in antiviral immunity
Authors: Lupfer Christopher , Kanneganti Thirumala‐Devi 
Published: August 2013

SummaryNucleotide oligomerization and binding domain (NOD)‐like receptors (NLRs) are a major constituent of the cytosolic innate immune‐sensing machinery and participate in a wide array of pathways including nuclear factor κB (NF‐κB), mitogen‐activated protein kinase (MAPK), inflammasome, and type I interferon (IFN) signaling. NLRs have known roles in autoimmune, autoinflammatory, and infectious diseases. With respect to virus infection, NLRP3 is the most extensively studied NLR, including mechanisms of activation and inhibition. Furthermore, the importance of NLRP3 in both innate and adaptive immunity has been demonstrated. In comparison to NLRP3, the roles of other NLRs during virus infection are only just emerging. NLRC2 is an important activator of innate antiviral signaling and was recently found to mitigate inflammation during virus infection through autophagy. Finally, functions for NLRX1 in immune modulation and reactive oxygen species production require further examination and the importance of NLRC5 as a transactivator of major histocompatibility complex (MHC) class I and antigen presentation is currently developing. In this review, we discuss current knowledge pertaining to viruses and NLRs as well as areas of potential research, which will help advance the study of NLR biology during virus infection.
Bugs in the system
Authors: Menachery Vineet D. , Baric Ralph S. 
Published: August 2013

SummaryImmunity to respiratory virus infection is governed by complex biological networks that influence disease progression and pathogenesis. Systems biology provides an opportunity to explore and understand these multifaceted interactions based on integration and modeling of multiple biological parameters. In this review, we describe new and refined systems‐based approaches used to model, identify, and validate novel targets within complex networks following influenza and coronavirus infection. In addition, we propose avenues for extension and expansion that can revolutionize our understanding of infectious disease processes. Together, we hope to provide a window into the unique and expansive opportunity presented by systems biology to understand complex disease processes within the context of infectious diseases.
The great balancing act: regulation and fate of antiviral T‐cell interactions
Authors: Moseman E. Ashley , McGavern Dorian B. 
Published: August 2013

SummaryThe fate of T lymphocytes revolves around a continuous stream of interactions between the T‐cell receptor (TCR) and peptide‐major histocompatibility complex (MHC) molecules. Beginning in the thymus and continuing into the periphery, these interactions, refined by accessory molecules, direct the expansion, differentiation, and function of T‐cell subsets. The cellular context of T‐cell engagement with antigen‐presenting cells, either in lymphoid or non‐lymphoid tissues, plays an important role in determining how these cells respond to antigen encounters. CD8+ T cells are essential for clearance of a lymphocytic choriomeningitis virus (LCMV) infection, but the virus can present a number of unique challenges that antiviral T cells must overcome. Peripheral LCMV infection can lead to rapid cytolytic clearance or chronic viral persistence; central nervous system infection can result in T‐cell‐dependent fatal meningitis or an asymptomatic carrier state amenable to immunotherapeutic clearance. These diverse outcomes all depend on interactions that require TCR engagement of cognate peptide‐MHC complexes. In this review, we explore the diversity in antiviral T‐cell behaviors resulting from TCR engagement, beginning with an overview of the immunological synapse and progressing to regulators of TCR signaling that shape the delicate balance between immunopathology and viral clearance.
The impact of macroautophagy on CD8+ T‐cell‐mediated antiviral immunity
Authors: Perot Brieuc P. , Ingersoll Molly A. , Albert Matthew L. 
Published: August 2013

SummaryMacroautophagy is a catabolic recycling pathway, which can be induced by various stress stimuli. Viruses are able to manipulate autophagy in the cells that they infect. The impact of autophagy on the innate immune response to viruses and its stimulatory role in antigen presentation to CD4+ T cells are well documented. Herein, we present the impact of autophagy on the activation of cytotoxic T lymphocyte (CTL)‐mediated antiviral immune responses, which are required for the eradication or control of multiple viruses. We first discuss the general mechanisms by which viruses can either induce or block autophagy in cells. We then explore the cross‐talk between autophagy and innate immune processes, which are both first line defenses against viruses; and constitute crucial steps for the initiation of potent adaptive immune responses. We describe the impact of autophagy on the presentation of viral peptide antigens on class I major histocompatibility complex (MHC I), a prerequisite for the priming of CTL responses. In sum, our review highlights the interplay between viruses and three integrated host response pathways – autophagy, innate and adaptive immunity – providing a framework for future mechanistic and pathogenesis‐based research.
Geographical variation in hurricane impacts among sea turtle populations
Authors: Dewald Julius R. , Pike David A. 
Published: August 2013

AbstractAimHurricanes bring wind and rainfall that can have dramatic effects on coastal ecosystems, which provide important nesting locations for some migratory species. We investigated the frequency with which hurricanes impact spatially and biologically distinct sea turtle nesting populations to understand whether the reproductive biology of sea turtles can buffer population‐level impacts of these disturbances.LocationNorth‐western Atlantic and north‐eastern Pacific Oceans.MethodsHistorical hurricane paths from 1970 to 2007 were combined into a spatial layer of seasonal storm frequency, which we used to quantify the frequency of impacts on sea turtle nesting sites. This was done by comparing spatio‐temporal patterns of hurricane frequency among nesting sites used by different species and spatially/biologically distinct populations (‘regional management units’).ResultsHurricanes affected 97% of sea turtle nesting beaches (n = 2444) over four decades, and the seasonal incidence of these storms overlapped substantially with sea turtle nesting and egg incubation periods. The spatial distribution of storms, in relation to the distribution of species and regional management units, determined relative exposure to large storm events. Green (Chelonia mydas), hawksbill (Eretmochelys imbricata) and leatherback (Dermochelys coriacea) turtle nesting beaches experienced relatively frequent storms; loggerhead (Caretta caretta) and Kemp's ridley (Lepidochelys kempii) turtle nesting beaches experienced relatively fewer storms; and olive ridley turtle (Lepidochelys olivacea) nesting sites were least affected.Main conclusionsExtreme weather events are common features of coastal environments and may impact sea turtles by altering nesting habitat quality (through sand erosion and accretion) and lowering within‐season reproductive success by drowning incubating embryos or eroding nests. The unique reproductive attributes of sea turtles (i.e. individual females reproduce at 2–5‐year intervals, and when reproducing lay 2–7 clutches of c. 100 large eggs at c. 2‐week intervals) may be uniquely suited to exploiting highly disturbed nesting habitats. The impacts of hurricanes on sea turtle populations may be limited because even in severe storm seasons only a proportion of adult females are reproducing, and only those eggs incubating at the time of storm impact will be directly affected. Understanding whether the frequency of large storms influences long‐term population dynamics will aid in the development of effective local and regional management plans for sea turtle recovery efforts.
Gonadal steroids regulate the expression of aggrecanases in human endometrial stromal cells in vitro
Authors: Wen Jiadi , Zhu Hua , Leung Peter C.K. 
Published: August 2013

AbstractThe human endometrium undergoes cyclic change during each menstrual cycle in response to gonadal steroids. Proteolysis of endometrial extracellular matrix (ECM) is necessary to prepare this dynamic tissue for pregnancy. Proteolytic enzymes such as matrix metalloproteinase (MMP) and closely related a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) have been assigned key roles in the highly regulated cyclic remodelling of the endometrial ECM. We have previously shown that ADAMTS‐1 undergoes spatiotemporal changes in human endometrial stromal cells under the regulation of gonadal steroids. This suggests that other ADAMTS subtypes, known as aggrecanases, may contribute to the ECM remodelling events that occur in female physiological cycles and in preparation for pregnancy. To determine whether progesterone (P4), 17β‐estradiol (E2), or dihydrotestosterone (DHT), alone or in combination, are capable of regulating ADAMTS‐4, ‐5, ‐8 or ‐9 expression in human endometrial stromal cells in vitro. Real‐time quantitative PCR and Western blot analysis were used to measure ADAMTSs mRNA and protein levels in primary cultures of human endometrial stromal cells (n = 12). P4, DHT but not E2 have regulatory effects on ADAMTS‐8, ‐9 and ‐5 expression. Combined treatment with gonadal steroids did not show any synergistic or antagonistic effects. However, the synthetic steroid antagonists RU486 and hydroxyflutamide specifically inhibited the P4‐ or DHT‐mediated regulatory effects on ADAMTS expression. These studies provide evidence that the regulation of aggrecanases by gonadal steroids in human endometrial stromal cells may play an important role during decidualization.
Periodontal disease and oral health‐related behavior as factors associated with preterm birth: a case–control study in south‐eastern Brazil
Authors: Macedo J. F. , Ribeiro R. A. , Machado F. C. , Assis N. M. S. P. , Alves R. T. , Oliveira A. S. , Ribeiro L. C. 
Published: August 2013

Background and ObjectiveSeveral studies have suggested a link between periodontal disease and preterm birth, but the mechanism of how this occurs remains controversial. Therefore, this study aimed to investigate whether periodontal disease, defined according to two commonly used clinical definitions, is associated with preterm birth and to examine the association regarding oral health‐related behaviors during pregnancy.Material and MethodsThis case–control study included women 18–40 years of age. Demographic and socio‐economic data, information on current and previous pregnancies, and data on dental health‐related behaviors and periodontal clinical parameters were collected within 48 h postpartum. Periodontal disease was assessed according to two definitions: four or more teeth with at least one site showing a probing depth of ≥ 4 mm and clinical attachment level of ≥ 3 mm (Definition 1); or at least one site with probing depth and clinical attachment level of ≥ 4 mm (Definition 2). The chi‐square test was used to examine differences in the proportion of categorical variables. Bivariate analysis was performed to analyze the proportion of preterm births with respect to independent variables. Multiple logistic regression analyses were used to assess the association between periodontal disease and preterm birth. Odds ratios (ORs) were calculated with a 95% confidence interval (95% CI).ResultsA total of 296 postpartum women met the inclusion criteria. The case group included 74 women who delivered a preterm neonate (< 37 wk of gestation) and the control group included 222 women with deliveries at term (≥ 37 wk). Periodontal disease according to Definition 1 was not associated with fewer weeks of gestation (adjusted OR (ORadjusted) = 1.62; 95% CI = 0.80–3.29; p = 0.178). However, a significant association was found between periodontal disease, according to Definition 2, and preterm birth (ORadjusted = 1.98; 95% CI = 1.14–3.43; p = 0.015). Increased appetite and a low number of daily toothbrushings were associated with preterm birth, regardless of the definition of periodontal disease used.ConclusionPeriodontal disease defined according to Definition 2 and unfavorable oral health‐related behavior were factors associated with preterm birth.
The Effects of Video Self‐Modeling on the Decoding Skills of Children at Risk for Reading Disabilities
Authors: Ayala Sandra M. , O'Connor Rollanda 
Published: August 2013

Ten first grade students who had responded poorly to a Tier 2 reading intervention in a response to intervention (RTI) model received an intervention of video self‐modeling to improve decoding skills and sight word recognition. Students were video recorded blending and segmenting decodable words and reading sight words. Videos were edited and viewed a minimum of four times per week. Data were collected twice per week using curriculum‐based measures. A single subject multiple baseline across participants design was used. Results indicated an increase in decoding skills and sight word recognition for all participants. A 2‐week posttest maintenance assessment showed retention or increases for 70 percent of participants. Results from the study offer promise for a specific intervention that may reach particular students who respond poorly to Tier 2 reading instruction.
The Science of the Individual
Authors: Rose L. Todd , Rouhani Parisa , Fischer Kurt W. 
Published: August 2013

ABSTRACTOur goal is to establish a science of the individual, grounded in dynamic systems, and focused on the analysis of individual variability. Our argument is that individuals behave, learn, and develop in distinctive ways, showing patterns of variability that are not captured by models based on statistical averages. As such, any meaningful attempt to develop a science of the individual necessarily begins with an account of the individual variability that is pervasive in all aspects of behavior, and at all levels of analysis. Using examples from fields as diverse as education and medicine, we show how starting with individual variability, not statistical averages, helped researchers discover two sources of ordered variability—pathways and contexts—that have implications for theory, research, and practice in multiple disciplines. We conclude by discussing three broad challenges—data, models, and the nature of science—that must be addressed to ensure that the science of the individual reaches its full potential.