Miracle-dz/UniFAR-FTUs huggingface dataset:
Juvenile hormone downregulates vitellogenin production in Ectatomma tuberculatum (Hymenoptera: Formicidae) sterile workers

ABSTRACT In the ant Ectatomma tuberculatum (Olivier 1792), workers have active ovaries and lay trophic eggs that are eaten by the queen and larvae. Vitellogenins are the main proteins found in the eggs of insects and are the source of nutrients for the embryo in the fertilized eggs and for adults in the trophic eggs. In social insects, vitellogenin titres vary between castes and affect reproductive social status, nursing, foraging, longevity, somatic maintenance, and immunity. In most insects, vitellogenin synthesis is mainly regulated by juvenile hormone. However, in non-reproductive worker ants, this relationship is poorly characterized. This study determined the effects of juvenile hormone on vitellogenin synthesis in non-reproductive E. tuberculatum workers. Juvenile hormone was topically applied onto workers, and the effect on vitellogenin synthesis in the fat body and vitellogenin titres in the haemolymph were analysed by ELISA and qPCR. Juvenile hormone downregulated protein synthesis and reduced vitellogenin titres in the haemolymph, suggesting that in workers of E. tuberculatum, juvenile hormone loses its gonadotrophic function. Summary: Juvenile hormone downregulates vitellogenin synthesis in worker ants producing trophic eggs.
Predictive modeling of non‐viral gene transfer

In non‐viral gene delivery, the variance of transgenic expression stems from the low number of plasmids successfully transferred. Here, we experimentally determine Lipofectamine‐ and PEI‐mediated exogenous gene expression distributions from single cell time‐lapse analysis. Broad Poisson‐like distributions of steady state expression are observed for both transfection agents, when used with synchronized cell lines. At the same time, co‐transfection analysis with YFP‐ and CFP‐coding plasmids shows that multiple plasmids are simultaneously expressed, suggesting that plasmids are delivered in correlated units (complexes). We present a mathematical model of transfection, where a stochastic, two‐step process is assumed, with the first being the low‐probability entry step of complexes into the nucleus, followed by the subsequent release and activation of a small number of plasmids from a delivered complex. This conceptually simple model consistently predicts the observed fraction of transfected cells, the cotransfection ratio and the expression level distribution. It yields the number of efficient plasmids per complex and elucidates the origin of the associated noise, consequently providing a platform for evaluating and improving non‐viral vectors. Biotechnol. Bioeng. 2010. 105: 805–813. © 2009 Wiley Periodicals, Inc.
Regulation and Function of the CD3γ DxxxLL Motif: A Binding Site for Adaptor Protein-1 and Adaptor Protein-2 in Vitro

Several receptors are downregulated by internalization after ligand binding. Regulation of T cell receptor (TCR) expression is an important step in T cell activation, desensitization, and tolerance induction. One way T cells regulate TCR expression is by phosphorylation/dephosphorylation of the TCR subunit clusters of differentiation (CD)3γ. Thus, phosphorylation of CD3γ serine 126 (S126) causes a downregulation of the TCR. In this study, we have analyzed the CD3γ internalization motif in three different systems in parallel: in the context of the complete multimeric TCR; in monomeric CD4/CD3γ chimeras; and in vitro by binding CD3γ peptides to clathrin-coated vesicle adaptor proteins (APs). We find that the CD3γ D127xxxLL131/132 sequence represents one united motif for binding of both AP-1 and AP-2, and that this motif functions as an active sorting motif in monomeric CD4/ CD3γ molecules independently of S126. An acidic amino acid is required at position 127 and a leucine (L) is required at position 131, whereas the requirements for position 132 are more relaxed. The spacing between aspartic acid 127 (D127) and L131 is crucial for the function of the motif in vivo and for AP binding in vitro. Furthermore, we provide evidence indicating that phosphorylation of CD3γ S126 in the context of the complete TCR induces a conformational change that exposes the DxxxLL sequence for AP binding. Exposure of the DxxxLL motif causes an increase in the TCR internalization rate and we demonstrate that this leads to an impairment of TCR signaling. On the basis of the present results, we propose the existence of at least three different types of L-based receptor sorting motifs.
Epithelial to mesenchymal transition (EMT) and airway remodelling after human lung transplantation

Background: Aberrant epithelial repair is a key event in the airway remodelling which characterises obliterative bronchiolitis (OB) in the transplanted lung. The potential for airway epithelium from lung transplant recipients to undergo epithelial to mesenchymal cell transition (EMT) was assessed in culture and in vivo in lung allograft tissue. Methods: Change in epithelial and mesenchymal marker expression was assessed after stimulation with transforming growth factor β1 (TGF-β1) alone or in combination with tumour necrosis factor α (TNFα) and compared with untreated controls. The ability of cells to deposit extracellular matrix, secrete matrix metalloproteinases (MMPs) and invade collagen was investigated. Immunolocalisation of epithelial and mesenchymal markers was compared in airway tissue from stable recipients and those with OB. Results: Untreated cells maintained epithelial morphology and phenotype. TGF-β1 reduced expression of epithelial markers, increased expression of vimentin and fibronectin, promoted collagen I and fibronectin deposition and increased MMP-9 production. Co-treatment with TNFα dramatically accentuated phenotypic and some functional features of EMT. Airway epithelial biopsies from recipients with OB demonstrated significantly increased staining for mesenchymal markers and significantly reduced E-cadherin staining compared with stable recipients. Conclusions: These observations demonstrate the ability of human airway epithelium to undergo EMT and suggest this phenomenon may be a potential link between inflammatory injury and TGF-β1-driven airway remodelling in the development of OB.
Perception of the moraic obstruent /Q/: a cross-linguistic study

Japanese natives segment speech into morae. The current study tested whether this extends to perception of geminate consonants. We hypothesized that Japanese natives rely on the moraic obstruent /Q/ that is represented as a silent duration when perceiving geminate consonants. If so, it should be more difficult for them to distinguish ‘geminate fricative consonants /ss/’ and ‘a silent duration plus singleton fricative consonant /_s/’. Two series of cross-linguistic experiments with Japanese and Dutch natives compared discrimination and categorization accuracy of pseudo words including /ss/ and /_s/. Japanese natives discriminated them well while they poorly categorized them. Dutch natives performed both tasks with regard to /_s/ relatively well. These result patterns support our hypothesis. This provides further support for the language specific listening.
A Pine Is a Pine and a Spruce Is a Spruce – The Effect of Tree Species and Stand Age on Epiphytic Lichen Communities

With an increasing demand for forest-based products, there is a growing interest in introducing fast-growing non-native tree species in forest management. Such introductions often have unknown consequences for native forest biodiversity. In this study, we examine epiphytic lichen species richness and species composition on the trunks of non-native Pinus contorta and compare these to the native Pinus sylvestris and Picea abies in managed boreal forests in northern Sweden across a chronosequence of age classes. Overall, we recorded a total of 66,209 lichen occurrences belonging to 57 species in the 96 studied forest stands. We found no difference in species richness of lichens between stands of P. contorta and P. sylvestris, but stands of P. abies had higher total species richness. However, species richness of lichens in stands of P. abies decreased with increasing stand age, while no such age effect was detected for P. contorta and P. sylvestris. Lichen species composition progressively diverged with increasing stand age, and in 30-year-old stands all three tree species showed species-specific assemblages. Epiphytic lichen assemblages in stands of 30-year-old P. contorta were influenced by greater basal area, canopy closure, and average diameter at breast height, P. abies stands by higher branch density and canopy closure, and stands of P. sylvestris by greater bark crevice depth. Differences in lichen species richness and composition were mainly explained by canopy closure and habitat availability, and the greater canopy closure in mature P. abies stands promoted the colonization and growth of calicioid lichen species. Our results indicate that the non-native P. contorta have similar species richness as the native P. sylvestris. The main difference in lichen species richness and composition is between P. abies and Pinus spp. in managed forests of boreal Sweden.
Structural Modeling of Protein Interactions by Analogy: Application to PSD-95

We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than comparative modeling and a higher accuracy than docking. It relies on structurally defined interactions of each of the complex components, or their homologs, with any other protein, irrespective of its fold. For each component, its known binding modes with other proteins of any fold are collected and expanded by the known binding modes of its homologs. These modes are then used to restrain conventional molecular docking, resulting in a set of binary domain complexes that are subsequently ranked by geometric complementarity and a statistical potential. The method is evaluated by predicting 20 binary complexes of known structure. It is able to correctly identify the binding mode in 70% of the benchmark complexes compared with 30% for protein docking. We applied comparative patch analysis to model the complex of the third PSD-95, DLG, and ZO-1 (PDZ) domain and the SH3-GK domains in the PSD-95 protein, whose structure is unknown. In the first predicted configuration of the domains, PDZ interacts with SH3, leaving both the GMP-binding site of guanylate kinase (GK) and the C-terminus binding cleft of PDZ accessible, while in the second configuration PDZ interacts with GK, burying both binding sites. We suggest that the two alternate configurations correspond to the different functional forms of PSD-95 and provide a possible structural description for the experimentally observed cooperative folding transitions in PSD-95 and its homologs. More generally, we expect that comparative patch analysis will provide useful spatial restraints for the structural characterization of an increasing number of binary and higher-order protein complexes.
The formation of the first galaxies and the transition to low-mass star formation

Abstract The formation of the first galaxies at redshifts z ~ 10−15 signaled the transition from the simple initial state of the universe to one of ever increasing complexity. We here review recent progress in understanding their assembly process with numerical simulations, starting with cosmological initial conditions and modelling the detailed physics of star formation. In this context we emphasize the importance and influence of selecting appropriate initial conditions for the star formation process. We revisit the notion of a critical metallicity resulting in the transition from primordial to present-day initial mass functions and highlight its dependence on additional cooling mechanisms and the exact initial conditions. We also review recent work on the ability of dust cooling to provide the transition to present-day low-mass star formation. In particular, we highlight the extreme conditions under which this transition mechanism occurs, with violent fragmentation in dense gas resulting in tightly packed clusters.
Influence of timing of sexual debut and first marriage on sexual behaviour in later life: findings from four survey rounds in the Kisesa cohort in northern Tanzania

Objectives: To evaluate quality of sexual debut and first marriage data, measure trends and study the association of risky sexual behaviour in youth with adult risk behaviour. Methods: Reports on age at first sex (AFS) and age at first marriage (AFM) from the Kisesa cohort study, 1994–2004, were evaluated for consistency and used to describe trends in median age-at-event and time spent single but sexually active in different birth cohorts. The association of these variables with marital stability and numbers of partners at later ages was explored using statistical regression techniques. Results: AFS and AFM were inconsistently reported by 32% and 33% of respondents, respectively, but there was no general tendency to report lower or higher ages at a later report date. In 10-year birth cohorts born between 1950–9 and 1980–9, male median AFS declined from 18.1 to 17.0 years and female median AFM rose from 16.2 to 16.6 years. Young people of both sexes currently spend longer sexually active but unmarried than previously. Early marriage is statistically associated with remarriage and polygamy; longer time between sexual debut and marriage is associated with higher numbers of partners at later stages of life. Conclusion: Inconsistent reporting of age-at-event introduces noise but does not bias estimates of population level indicators. Lengthening time spent single and sexually active suggests that men and women entering first marriage will have been exposed to increased numbers of non-marital partners. Successful youth interventions may also influence adult behaviour.
PlanHab: Hypoxia counteracts the erythropoietin suppression, but seems to exaggerate the plasma volume reduction induced by 3 weeks of bed rest

The study examined the distinct and synergistic effects of hypoxia and bed rest on the erythropoietin (EPO) concentration and relative changes in plasma volume (PV). Eleven healthy male lowlanders underwent three 21‐day confinement periods, in a counterbalanced order: (1) normoxic bed rest (NBR; PIO2: 133.1 ± 0.3 mmHg); (2) hypoxic bed rest (HBR; PIO2: 90.0 ± 0.4 mmHg, ambient simulated altitude of ~4000 m); and (3) hypoxic ambulation (HAMB; PIO2: 90.0 ± 0.4 mmHg). Blood samples were collected before, during (days 2, 5, 14, and 21) and 2 days after each confinement to determine EPO concentration. Qualitative differences in PV changes were also estimated by changes in hematocrit and hemoglobin concentration along with concomitant changes in plasma renin concentration. NBR caused an initial reduction in EPO by ~39% (P = 0.04). By contrast, HBR enhanced EPO (P = 0.001), but the increase was less than that induced by HAMB (P < 0.01). All three confinements caused a significant reduction in PV (P < 0.05), with a substantially greater drop in HBR than in the other conditions (P < 0.001). Thus, present results suggest that hypoxia prevents the EPO suppression, whereas it seems to exaggerate the PV reduction induced by bed rest.
“Fairy rings” of participation: the invisible network influencing participation in online communities

Individuals participate in many different ways in online communities. There is an extensive body of research describing participation as a key metaphor in communities of practice and stressing that participatory mobility is influenced by underground multidirectional activities, directed away from the notion of periphery to the centre practices and taking the shape of expansive swarming and multidirectional pulsations. This article describes an ongoing observational study proposing a model that attempts to determine how users participate in online communities and what influences them to alter the way in which they participate. We performed daily observations on user participatory behaviour in 50 online communities using public domain – anonymous data available in the communities. The specific communities were selected because they are related to learning and support learning activities within their networks. The data observations collected were analysed using Compendium, a hypermedia knowledge mapping and sense-making tool, to represent and structure the data, make complex cross data queries, test hypotheses and build representation of real examples to support our claims. Initial findings indicate that users connect, participate, contribute and collaborate on a shared objective, transferring information and pooling knowledge within and between communities in four different modes. During their online journey, users switched between modes of participation or even remained in one specific mode, implying that the way in which users participate in an online community is not just related to the mode of participation and the level of engagement with the community but it is also due to hidden reasons or motivations, an invisible network of interactions of elements that affect the willingness of the user to participate. This layer is not immediately evident in the user actions but can be inferred by analysing user reactions. It is argued that user participation in online communities occurs in two layers; the “visible” layer of participation with the different modes; and the “invisible” layer of element interactions, similar to formations observed in nature when a radically spreading underground network of fungi activity results in a ring or arc formation of mushrooms, also known as a “fairy ring”. These underground multidirectional activities influence participation and participatory mobility. Following an open scientific inquiry approach and an open research paradigm we plan to share these observations with a wider audience of practitioners, researchers and theorists for all to test or contest our arguments, and to enrich, question, or support our model.
Effect of Interfacial Strength on Erosion Behavior of FRPs

Experiments were carried out to study the effect of interfacial strength between a matrix material and fibers on the solid particle erosion behavior of FRPs. The FRPs used were epoxy resins unidirectionally reinforced by carbon fibers. Although more than ten papers have been published concerning the erosion behaviors of FRPs, it has not been clarified how the interfacial strength between a matrix material and fibers affects the erosion behavior of FRPs. In the present erosion experiments, FRPs with treated fibers or untreated fibers were used as test materials to examine the effect of interfacial strength between a matrix material and fibers on the erosion rate. According to the tensile tests, the FRPs with treated fibers show higher interfacial strength between a matrix material and fibers than the FRPs with untreated fibers. The results of the erosion tests show that the FRPs with treated fibers have higher erosion resistance than the FRPs with untreated fibers due to higher interfacial strength between a matrix material and fibers.
Bayes Linear Calibrated Prediction for Complex Systems

A calibration-based approach is developed for predicting the behavior of a physical system that is modeled by a computer simulator. The approach is based on Bayes linear adjustment using both system observations and evaluations of the simulator at parameterizations that appear to give good matches to those observations. This approach can be applied to complex high-dimensional systems with expensive simulators, where a fully Bayesian approach would be impractical. It is illustrated with an example concerning the collapse of the thermohaline circulation (THC) in the Atlantic Ocean.
Biotransformation enzymes in the rodent nasal mucosa: the value of a histochemical approach.

An increasing number of chemicals have been identified as being toxic to the nasal mucosa of rats. While many chemicals exert their effects only after inhalation exposure, others are toxic following systemic administration, suggesting that factors other than direct deposition on the nasal mucosa may be important in mechanisms of nasal toxicity. The mucosal lining of the nasal cavity consists of a heterogeneous population of ciliated and nonciliated cells, secretory cells, sensory cells, and glandular and other cell types. For chemicals that are metabolized in the nasal mucosa, the balance between metabolic activation and detoxication within a cell type may be a key factor in determining whether that cell type will be a target for toxicity. Recent research in the area of xenobiotic metabolism in nasal mucosa has demonstrated the presence of many enzymes previously described in other tissues. In particular, carboxylesterase, aldehyde dehydrogenase, cytochromes P-450, epoxide hydrolase, and glutathione S-transferases have been localized by histochemical techniques. The distribution of these enzymes appears to be cell-type-specific and the presence of the enzyme may predispose particular cell types to enhanced susceptibility or resistance to chemical-induced injury. This paper reviews the distribution of these enzymes within the nasal mucosa in the context of their contribution to xenobiotic metabolism. The localization of the enzymes by histochemical techniques has provided important information on the potential mechanism of action of esters, aldehydes, and cytochrome P-450 substrates known to injure the nasal mucosa. ImagesPLATE 1.PLATE 2.PLATE 3.
A Dynamic Analysis of a Demand Curve-Based Capacity Market Proposal: The PJM Reliability Pricing Model

Because of high generation adequacy standards in the power industry, some peaking capacity operates for a limited time during the year and may not receive sufficient energy revenues to meet its fixed costs. This is particularly true when energy prices are capped in order to mitigate market power. The northeastern U.S. independent system operators (ISOs) have responded to this issue by establishing capacity obligations for loads and markets for installed capacity, thus providing a capacity revenue stream to generators. The installed capacity (ICAP) markets in the northeastern U.S. markets are a response to this need for additional incentives to construct generation. The Federal Energy Regulatory Commission (FERC) has accepted the PJM Interconnection's (PJM) proposal to replace the present fixed ICAP requirement that is placed upon load serving entities (LSEs) with a demand curve-based system in which the ISO would be responsible for acquiring "residual" capacity on behalf of LSEs. The demand curve approach pays more when reserve margins are smaller and provides a reduced incentive for investment when installed reserves are above the target. Another goal is to make revenues more predictable for generators, making investment less costly and, ultimately, lowering prices for consumers. A dynamic representative agent model is presented for projecting effects upon reserve margins, generator profitability, and consumer costs and is applied to alternative demand curves proposed for the PJM market. The consumer costs resulting from a sloped demand curve are robustly lower compared to the present fixed requirement under a wide range of assumptions concerning behavior of generation owners, including risk attitudes, bidding behavior, and willingness to build capacity as a function of forecast profit. The cost savings arise from lower capital costs to generators due to reduced risk and risk premiums. Also, average installed capacity is less for the same level of reliability because of reduced fluctuations in installed reserves