bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Advance: Actin CytoFRET, a novel FRET flow cytometry method for detection of actin dynamics in resting and activated T cell
Authors: Larbret Frédéric , Dubois Nicholas , Brau Frédéric , Guillemot Elodie , Mahiddine Karim , Tartare-Deckert Sophie , Verhasselt Valérie , Deckert Marcel 
Published: June 2013

ABSTRACTActin cytoskeleton plays a critical role in regulating T cell motility and activation. However, the lack of a real-time quantitative method to analyze actin assembly has limited the progress toward understanding actin regulation. Here, we describe a novel approach to probe actin dynamics on living T cells using FRET combined with flow cytometry. We have first generated a Jurkat T cell line stably coexpressing EGFP and mOrange FPs fused to actin. The real-time variation of actin monomer assembly or disassembly into filaments was quantified using a ratiometric flow cytometry method measuring changes in the mOrange/EGFP emission ratio. The method was validated on resting T cells by using chemical compounds with known effects on actin filaments and comparison with conventional microscopy imaging. Our method also detected the rapid and transient actin assembly in T cells stimulated by anti-CD3/CD28-coated beads, demonstrating its robustness and high sensitivity. Finally, we provide evidence that lentiviral-mediated transduction of shRNAs in engineered Jurkat cells could be used as a strategy to identify regulators of actin remodeling. In conclusion, the flow cytometric FRET analysis of actin polymerization represents a new technical advance to study the dynamics of actin regulation in intact cells.
Modulation of granulocyte kinetics by GM-CSF/IFN-γ in a human LPS rechallenge model
Authors: Kamp Vera M , Leentjens Jenneke , Pillay Janesh , Langereis Jeroen D , de Kleijn Stan , Kox Matthijs , Netea Mihai G , Pickkers Peter , Koenderman Leo 
Published: June 2013

ABSTRACTInflammation in response to infection or trauma can lead to CARS, which is characterized by leukocyte dysfunction. In this study, we used a human model system for CARS to study the effect of GM-CSF and IFN-γ treatment on this immunoparalyzed state. Healthy human volunteers were treated with GM-CSF (4 μg/kg), IFN-γ (100 μg), or placebo in between two challenges with Escherichia coli LPS/endotoxin (2 ng/kg). Serial leukocyte blood counts were measured. Neutrophil subsets were discriminated using CD16 and CD62L expression. LPS rechallenge resulted in increased mobilization of mature neutrophils, whereas banded neutrophils decreased. GM-CSF and IFN-γ treatment did not restore these changes. GM-CSF treatment did, however, increase the number of CD16bright/CD62Ldim neutrophils that were previously shown be able to suppress T cell proliferation. IFN-γ treatment decreased neutrophilia seen after LPS rechallenge. Our study shows that LPS rechallenge was associated with changes in the distribution of neutrophil subsets, whereas no additional changes in kinetics of other granulocyte populations were observed. GM-CSF and IFN-γ treatment induced a shift in granulocyte composition toward an anti-inflammatory direction by increasing CD16bright/CD62Ldim cells or decreasing neutrophil counts, respectively.
RIP2 activity in inflammatory disease and implications for novel therapeutics
Authors: Jun Janice C , Cominelli Fabio , Abbott Derek W 
Published: June 2013

ABSTRACTThe role of NOD2 and RIP2 in inflammatory disease has been paradoxical. Whereas loss-of-function NOD2 polymorphisms cause CD, a granulomatous disease of the gastrointestinal tract, gain-of-function mutations cause EOS—a granulomatous disease primarily affecting the skin, joints, and eyes. Thus, gain-of-function mutations and loss-of-function polymorphisms cause granulomatous inflammatory disease, only in different anatomic locations. The situation is complicated further by the fact that WT NOD2 and WT RIP2 activity has been implicated in diseases such as asthma, inflammatory arthritis and MS. This article reviews the role that the NOD2:RIP2 complex plays in inflammatory disease, with an emphasis on the inhibition of this signaling pathway as a novel pharmaceutical target in inflammatory disease.
Mannose receptor and macrophage galactose-type lectin are involved inBordetella pertussismast cell interaction
Authors: Vukman Krisztina V , Ravidà Alessandra , Aldridge Allison M , O'Neill Sandra M 
Published: June 2013

ABSTRACTMast cells are crucial in the development of immunity against Bordetella pertussis, and the function of TLRs in this process has been investigated. Here, the interaction between mast cells and B. pertussis with an emphasis on the role of CLRs is examined. In this study, two CLRs, MGL and MR, were detected for the first time on the surface of mast cells. The involvement of MR and MGL in the stimulation of mast cells by heat-inactivated BP was investigated by the use of blocking antibodies and specific carbohydrate ligands. The cell wall LOS of BP was also isolated to explore its role in this interaction. Mast cells stimulated with heat-inactivated BP or BP LOS induced TNF-α, IL-6, and IFN-γ secretion, which was suppressed by blocking MR or MGL. Inhibition of CLRs signaling during BP stimulation affected the ability of mast cells to promote cytokine secretion in T cells but had no effect on the cell-surface expression of ICAM1. Blocking MR or MGL suppressed BP-induced NF-κB expression but not ERK phosphorylation. Syk was involved in the CLR-mediated activation of mast cells by BP. Bacterial recognition by immune cells has been predominantly attributed to TLRs; in this study, the novel role of CLRs in the BP–mast cell interaction is highlighted.
Enhancing the low-frequency amplitude of ground force from a seismic vibrator through reduction of harmonic distortion
Authors: Wei Zhouhong , Phillips Thomas F. 
Published: June 2013

Extending the vibroseis bandwidth toward low frequencies (below 10 Hz) can bring many benefits for land seismic exploration such as deeper signal penetration and for near-surface inversion techniques. Due to physical limitations in vibrator mechanical and hydraulic systems, the ground force output from a vibrator at low frequencies is limited. This limited ground force output is severely distorted by harmonic distortion such that the ground force in fundamental frequencies is reduced. We focused on reducing harmonic distortion through vibrator control algorithms to improve vibrator performance at low frequencies. The purpose was to show that with only vibrator control algorithms, the fundamental ground force from a vibrator can be noticeably improved at low frequencies. In addition, we demonstrated a synthetic case using the weighted-sum ground force to simulate slip-sweep acquisition. Presumably, reducing source generated harmonic distortion can help decrease the slip time in slip-sweep operations thereby increasing productivity rates.
Effect of nutrient limitation of cyanobacteria on protease inhibitor production and fitness ofDaphnia magna
Authors: Schwarzenberger Anke , Sadler Thomas , Von Elert Eric 
Published: June 2013

SummaryHerbivore-plant interactions have been well studied in both terrestrial and aquatic ecosystems as they are crucial for the trophic transfer of energy and matter. In nutrient-rich freshwater ecosystems, the interaction between primary producers and herbivores is to a large extent represented by Daphnia and cyanobacteria. The occurrence of cyanobacterial blooms in lakes and ponds has, at least partly, been attributed to cyanotoxins, which negatively affect the major grazer of planktonic cyanobacteria, i.e. Daphnia. Among these cyanotoxins are the wide-spread protease inhibitors. These inhibitors have been shown (both in vitro and in situ) to inhibit the most important group of digestive proteases in the gut of Daphnia, i.e. trypsins and chymotrypsins, and to reduce Daphnia growth. In this study we grew cultures of the cyanobacterium Microcystis aeruginosa strain BM25 on nutrient replete, N-depleted or P-depleted medium. We identified three different micropeptins to be the cause for the inhibitory activity of BM25 against chymotrypsins. The micropeptin content depended on nutrient availability: Whereas N-limitation led to a lower concentration of micropeptins per biomass, P-limitation resulted in a higher production of these chymotrypsin inhibitors. The altered micropeptin content of BM25 was accompanied by changed effects on the fitness of Daphnia: A higher content of micropeptins led to lower IC50 values for Daphnia gut proteases and vice-versa. Following expectations, the lower content of micropeptins in the N-depleted BM25 caused higher somatic growth of Daphnia. Therefore, protease inhibitors can be regarded as a nutrient-dependent defence against grazers. Interestingly, although the P-limitation of the cyanobacterium led to a higher micropeptin content, high growth of D. magna was observed when they were fed with P-depleted BM25. This might be due to reduced digestibility of P-depleted cells with putatively thick mucilaginous sheaths. These findings indicate that both the grazer and the cyanobacterium benefit from P-reduction in light of digestibility and growth inhibition, which is an interesting starting point for further studies.
Glycemic Control in the 12 Months following a Change to SI Hemoglobin A1c Reporting Units
Authors: Kilpatrick Eric S , Rigby Alan S , Atkin Stephen L , Barth Julian H 
Published: June 2013

BACKGROUND
Many countries have implemented, or are considering, a change in hemoglobin A1c (Hb A1c) units from traditional percentage values [Diabetes Control and Complications Trial (DCCT)] to the new Système International d'Unités (SI) unit in millimoles per mole. Concern exists that such a large alteration in numeric values might lead, through confusion, to a deterioration in patients' glycemia. This study has assessed Hb A1c in the year before and after the change of units in a UK diabetes population.

METHODS
The Hb A1c in the 12 months immediately before the unit change (October 2010 to September 2011) was compared with the 12 months after (October 2011 to September 2012). Also, the subsequent change in Hb A1c in patients who had poor glycemic control [Hb A1c &gt;8% (64 mmol/mol)], either before or after the unit change, was compared.

RESULTS
Over the 2 years, 44 721 Hb A1c measurements were requested on 13 197 (7247 male, 5950 female) known diabetes patients. The population Hb A1c was no different between years, with a median [interquartile range (IQR)] value of 7.5% (6.6%–8.7%) after the change and 7.5% (6.5–8.7) before (P = 0.34). The subsequent change in Hb A1c following a raised (&gt;8%) result was the same regardless of whether the initial value reported was in DCCT or SI units [median (IQR) change in Hb A1c −0.2% (−0.9% to 0.3%), n = 4316, following a DCCT result, vs −0.2% (−0.8% to 0.3%), n = 4396, following SI; P = 0.44].

CONCLUSIONS
In this UK diabetes population, a move to SI Hb A1c reporting did not lead to any marked short-term deterioration in glycemia or a different Hb A1c outcome in patients with initial poor glucose control.
From algebraic cobordism to motivic cohomology
Authors: Hoyois Marc 
Published: June 2013

Abstract

Let S be an essentially smooth scheme over a field of characteristic exponent c.
We prove that there is a canonical equivalence of motivic spectra over S
MGL/(a
1,a
2,...)[1/c] ≃ Hℤ[1/c]
where Hℤ is the motivic cohomology spectrum, MGL is the algebraic cobordism spectrum, and the elements an
are generators of the Lazard ring. We discuss several applications including the computation of the slices of ℤ[1/c]-local Landweber exact motivic spectra and the convergence of the associated slice spectral sequences.
Phospho-Regulation Pathways During Egg Activation in Drosophila melanogaster
Authors: Krauchunas Amber R , Sackton Katharine L , Wolfner Mariana F 
Published: June 2013

Abstract
Egg activation is the series of events that transition a mature oocyte to an egg capable of supporting embryogenesis. Increasing evidence points toward phosphorylation as a critical regulator of these events. We used Drosophila melanogaster to investigate the relationship between known egg activation genes and phosphorylation changes that occur upon egg activation. Using the phosphorylation states of four proteins—Giant Nuclei, Young Arrest, Spindly, and Vap-33-1—as molecular markers, we showed that the egg activation genes sarah, CanB2, and cortex are required for the phospho-regulation of multiple proteins. We show that an additional egg activation gene, prage, regulates the phosphorylation state of a subset of these proteins. Finally, we show that Sarah and calcineurin are required for the Anaphase Promoting Complex/Cyclosome (APC/C)-dependent degradation of Cortex following egg activation. From these data, we present a model in which Sarah, through the activation of calcineurin, positively regulates the APC/C at the time of egg activation, which leads to a change in phosphorylation state of numerous downstream proteins.
UP-TORR: Online Tool for Accurate and Up-to-Date Annotation of RNAi Reagents
Authors: Hu Yanhui , Roesel Charles , Flockhart Ian , Perkins Lizabeth , Perrimon Norbert , Mohr Stephanie E 
Published: June 2013

Abstract
RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent–gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent–gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.
Genome-Wide Variation of Cytosine Modifications Between European and African Populations and the Implications for Complex Traits
Authors: Moen Erika L , Zhang Xu , Mu Wenbo , Delaney Shannon M , Wing Claudia , McQuade Jennifer , Myers Jamie , Godley Lucy A , Dolan M Eileen , Zhang Wei 
Published: June 2013

AbstractElucidating cytosine modification differences between human populations can enhance our understanding of ethnic specificity in complex traits. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at a false discovery rate of 1%. The CpG sites with greater modification levels in European descent were enriched in the proximal regulatory regions, while those greater in African descent were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained primarily by local genetic variation. In addition, a substantial proportion of local modification quantitative trait loci exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interactions could be common. Distinct correlations were observed between gene expression levels and cytosine modifications in proximal regions and gene bodies, suggesting epigenetic regulation of interindividual expression variation. Furthermore, quantitative trait loci associated with population-specific modifications can be colocalized with expression quantitative trait loci and single nucleotide polymorphisms previously identified for complex traits with known racial disparities. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.
Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?
Authors: dos Reis Mario , Yang Ziheng 
Published: June 2013

Abstract
Several studies have reported a negative correlation between estimates of the nonsynonymous to synonymous rate ratio (ω = dN/dS) and the sequence distance d in pairwise comparisons of the same gene from different species. That is, more divergent sequences produce smaller estimates of ω. Explanations for this negative correlation have included segregating nonsynonymous polymorphisms in closely related species and nonlinear dynamics of the ratio of two random variables. Here we study the statistical properties of the maximum-likelihood estimates of ω and d in pairwise alignments and explore the possibility that the negative correlation can be entirely explained by those properties. We show that the ω estimate is positively biased for small d and that the bias decreases with the increase of d. We also show that the estimates of ω and d are negatively correlated when ω &lt; 1 and positively correlated when ω &gt; 1. However, the bias in estimates of ω and the correlation between estimates of ω and d are not enough to explain the much stronger correlation observed in real data sets. We then explore the behavior of the estimates when the model is misspecified and suggest that the observed correlation may be due to protein-level selection that causes very different amino acids to be favored in different domains of the protein. Widely used models fail to account for such among-site heterogeneity and cause underestimation of the nonsynonymous rate and ω, with the bias being much stronger for distant sequences. We point out that tests of positive selection based on the ω ratio are invariant to the parameterization of the model and thus unaffected by bias in the ω estimates or the correlation between estimates of ω and d.
A DNA Damage Checkpoint Pathway Coordinates the Division of Dikaryotic Cells in the Ink Cap MushroomCoprinopsis cinerea
Authors: de Sena-Tomás Carmen , Navarro-González Mónica , Kües Ursula , Pérez-Martín José 
Published: June 2013

AbstractThe fungal fruiting body or mushroom is a multicellular structure essential for sexual reproduction. It is composed of dikaryotic cells that contain one haploid nucleus from each mating partner sharing the same cytoplasm without undergoing nuclear fusion. In the mushroom, the pileus bears the hymenium, a layer of cells that includes the specialized basidia in which nuclear fusion, meiosis, and sporulation occur. Coprinopsis cinerea is a well-known model fungus used to study developmental processes associated with the formation of the fruiting body. Here we describe that knocking down the expression of Atr1 and Chk1, two kinases shown to be involved in the response to DNA damage in a number of eukaryotic organisms, dramatically impairs the ability to develop fruiting bodies in C. cinerea, as well as other developmental decisions such as sclerotia formation. These developmental defects correlated with the impairment in silenced strains to sustain an appropriated dikaryotic cell cycle. Dikaryotic cells in which chk1 or atr1 genes were silenced displayed a higher level of asynchronous mitosis and as a consequence aberrant cells carrying an unbalanced dose of nuclei. Since fruiting body initiation is dependent on the balanced mating-type regulator doses present in the dikaryon, we believe that the observed developmental defects were a consequence of the impaired cell cycle in the dikaryon. Our results suggest a connection between the DNA damage response cascade, cell cycle regulation, and developmental processes in this fungus.
The Jaw of the Worm: GTPase-activating Protein EAT-17 Regulates Grinder Formation in Caenorhabditis elegans
Authors: Straud Sarah , Lee Inhwan , Song Bomi , Avery Leon , You Young-Jai 
Published: June 2013

Abstract
Constitutive transport of cellular materials is essential for cell survival. Although multiple small GTPase Rab proteins are required for the process, few regulators of Rabs are known. Here we report that EAT-17, a novel GTPase-activating protein (GAP), regulates RAB-6.2 function in grinder formation in Caenorhabditis elegans. We identified EAT-17 as a novel RabGAP that interacts with RAB-6.2, a protein that presumably regulates vesicle trafficking between Golgi, the endoplasmic reticulum, and plasma membrane to form a functional grinder. EAT-17 has a canonical GAP domain that is critical for its function. RNA interference against 25 confirmed and/or predicted RABs in C. elegans shows that RNAi against rab-6.2 produces a phenotype identical to eat-17. A directed yeast two-hybrid screen using EAT-17 as bait and each of the 25 RAB proteins as prey identifies RAB-6.2 as the interacting partner of EAT-17, confirming that RAB-6.2 is a specific substrate of EAT-17. Additionally, deletion mutants of rab-6.2 show grinder defects identical to those of eat-17 loss-of-function mutants, and both RAB-6.2 and EAT-17 are expressed in the terminal bulb of the pharynx where the grinder is located. Collectively, these results suggest that EAT-17 is a specific GTPase-activating protein for RAB-6.2. Based on the conserved function of Rab6 in vesicular transport, we propose that EAT-17 regulates the turnover rate of RAB-6.2 activity in cargo trafficking for grinder formation.
Teaching Interviewing Skills to Pediatric House Officers
Authors: Farsad Parichehr , Galliguez Pilarita , Chamberlin Robert , Roghmann Klaus J. 
Published: June 2013

Interviewing skills of 34 pediatric house officers were compared with those of five practicing members of the clinical faculty. Interviews with a programmed mother were videotaped to evaluate physician-patient interaction, data gathering, hypothesis formation and provision of therapy education, reassurance, support, and anticipatory guidance. In addition, eight pediatric interns (PL-1s) were assigned to a study group and five to a control group at the beginning of their outpatient department rotation. The study group received feedback after the videotaped interviews and a 1½-hour didactic session designed to teach interviewing skills. The control group received neither feedback nor the didactic session. Both groups were reevaluated at the end of the outpatient department rotation, again using the video-taped interview technique.
Results showed that data-gathering ability increased significantly; that the focus of attention shifted from a more disease-oriented to a more patient-oriented interview; that data were obtained by means of less direct, less leading questions; and that more support and reassurance were provided as the level of training and experience increased. After the outpatient department rotation, members of both the study group and the control group of PL-ls had improved significantly and approached the proficiency level of practicing pediatricians.