bluuebunny/crossref_metadata_2025_split huggingface dataset:
EVIDENCE OF QUASI-LINEAR SUPER-STRUCTURES IN THE COSMIC MICROWAVE BACKGROUND AND GALAXY DISTRIBUTION
Authors: Inoue Kaiki Taro , Sakai Nobuyuki , Tomita Kenji 
Published: October 2010

ABSTRACT
Recent measurements of hot and cold spots on the cosmic microwave background (CMB) sky suggest the presence of super-structures on (>100 h
−1 Mpc) scales. We develop a new formalism to estimate the expected amplitude of temperature fluctuations due to the integrated Sachs–Wolfe (ISW) effect from prominent quasi-linear structures. Applying the developed tools to the observed ISW signals from voids and clusters in catalogs of galaxies at redshifts z < 1, we find that they indeed imply a presence of quasi-linear super-structures with a comoving radius of 100 ∼ 300 h
−1 Mpc and a density contrast |δ| ∼ O(0.1). We also find that the observed ISW signals are at odds with the concordant Λ cold dark matter model that predicts Gaussian primordial perturbations at ≳3σ level. We confirm that the mean temperature around the CMB cold spot in the southern Galactic hemisphere filtered by a compensating top-hat filter deviates from the mean value at ∼3σ level, implying that a quasi-linear supervoid or an underdensity region surrounded by a massive wall may reside at low redshifts z < 0.3 and the actual angular size (16°–17°) may be larger than the apparent size (4°–10°) discussed in literature. Possible solutions are briefly discussed.
A diffusive air plasma in bi-directional nanosecond pulsed dielectric barrier discharge
Authors: Yang De-Zheng , Wang Wen-Chun , Li Shou-Zhe , Song Ying , Nie Dong-Xia 
Published: October 2010

In this study, a diffuse dielectric barrier discharge in air is generated by a bi-directional nanosecond pulsed power supply using a needle–plate electrode configuration at atmospheric pressure. Time-resolved spectra of N2(C
3Πu → B
3Πg, 0–0, 337.1 nm) for both positive and negative pulse discharges are recorded under severe electromagnetic interference. It is found that the lagged time of the photocurrent pulse compared with the voltage pulse in the negative pulse discharge is about 50 times longer than that in the positive pulse discharge at 16 kV pulse peak voltage and becomes shorter with an increase in pulse peak voltage. In addition, the gas temperature of the air plasma is determined to be approximately 395 K by measuring the optical emission spectra of the first negative band of
, 0–0, 391.4 nm).
Identification of subfamily-specific sites based on active sites modeling and clustering
Authors: de Melo-Minardi Raquel C. , Bastard Karine , Artiguenave François 
Published: October 2010

Abstract
Motivation: Current computational approaches to function prediction are mostly based on protein sequence classification and transfer of annotation from known proteins to their closest homologous sequences relying on the orthology concept of function conservation. This approach suffers a major weakness: annotation reliability depends on global sequence similarity to known proteins and is poorly efficient for enzyme superfamilies that catalyze different reactions. Structural biology offers a different strategy to overcome the problem of annotation by adding information about protein 3D structures. This information can be used to identify amino acids located in active sites, focusing on detection of functional polymorphisms residues in an enzyme superfamily. Structural genomics programs are providing more and more novel protein structures at a high-throughput rate. However, there is still a huge gap between the number of sequences and available structures. Computational methods, such as homology modeling provides reliable approaches to bridge this gap and could be a new precise tool to annotate protein functions.
Results: Here, we present Active Sites Modeling and Clustering (ASMC) method, a novel unsupervised method to classify sequences using structural information of protein pockets. ASMC combines homology modeling of family members, structural alignment of modeled active sites and a subsequent hierarchical conceptual classification. Comparison of profiles obtained from computed clusters allows the identification of residues correlated to subfamily function divergence, called specificity determining positions. ASMC method has been validated on a benchmark of 42 Pfam families for which previous resolved holo-structures were available. ASMC was also applied to several families containing known protein structures and comprehensive functional annotations. We will discuss how ASMC improves annotation and understanding of protein families functions by giving some specific illustrative examples on nucleotidyl cyclases, protein kinases and serine proteases.
Availability: http://www.genoscope.fr/ASMC/.
Contact: raquelcm@dcc.ufmg.br; kbastard@genoscope.cns.fr; artigue@genoscope.cns.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
The Human Carotid Body
Authors: Fagerlund Malin Jonsson , Kåhlin Jessica , Ebberyd Anette , Schulte Gunnar , Mkrtchian Souren , Eriksson Lars I. 
Published: October 2010

Background
Hypoxia is a common cause of adverse events in the postoperative period, where respiratory depression due to residual effects of drugs used in anesthesia is an important underlying factor. General anesthetics and neuromuscular blocking agents reduce the human ventilatory response to hypoxia. Although the carotid body (CB) is the major oxygen sensor in humans, critical oxygen sensing and signaling pathways have been investigated only in animals so far. Thus, the aim of this study was to characterize the expression of key genes and localization of their products involved in the human oxygen sensing and signaling pathways with a focus on receptor systems and ion channels of relevance in anesthesia.

Methods
Six CBs were removed unilaterally from patients undergoing radical neck dissection. The gene expression and cell-specific protein localization in the CBs were investigated with DNA microarrays, real-time polymerase chain reaction, and immunohistochemistry.

Results
We found gene expression of the oxygen-sensing pathway, heme oxygenase 2, and the K channels TASK (TWIK-related acid sensitive K channel)-1 and BK (large-conductance potassium channel). In addition, we show the expression of critical receptor subunits such as γ-aminobutyric acid A (α2, β3, and γ2), nicotinic acetylcholine receptors (α3, α7, and β2), purinoceptors (A2A and P2X2), and the dopamine D2 receptor.

Conclusions
In unique samples of the human CB, we here demonstrate presence of critical proteins in the oxygen-sensing and signaling cascade. Our findings demonstrate similarities to, but also important differences from, established animal models. In addition, our work establishes an essential platform for studying the interaction between anesthetic drugs and human CB chemoreception.
A computational study of the molecular and crystal structure and selected physical properties of octahydridosilasequioxane–(Si2O3H2)4. I. Electronic and structural aspects
Authors: Schutte C. J. H. , Pretorius J. A. 
Published: October 2010

The free molecule octahydridosilasequioxane, Si8O12H8, was computationally studied, as well as embedded in the unit cell. The point group of the free molecule is indeedOh, and its crystal symmetry is reduced toC3i, thus confirming the occurrence of two different types of Si−O−Si bond lengths found experimentally. The molecular orbitals of the free molecule show that some electron density occurs in the cubic cavity, thus contributing to the opening of the Si−O−Si angle. A study of the packing in the unit cell identifies a new type of packing scheme in which eight (partial) molecules participate: each apex H atom of one protruding Si−H bond of every molecule points to the corner of anequilateraltriangle having 2.631 Å sides. All hydrogen atoms in both the free molecule and in the solid state carry negative partial charges. The reason for this is also explored, as well as its consequences for the unique packing scheme.
Qualitative research in nutrition and dietetics: getting started
Authors: Swift J. A. , Tischler V. 
Published: October 2010

AbstractQualitative research is well placed to answer complex questions about food‐related behaviour because it investigates how and why individuals act in certain ways. The field of qualitative health research is undoubtedly gaining momentum and, increasingly, there is a recognition that it should be a vital part of the decision‐making processes that direct the development of health policy and practice. Much of the guidance available, however, is difficult to navigate for those new to ‘qualitative research’, and there is little discussion of qualitative research issues specifically in relation to nutrition and dietetics. This review, the first in a series, outlines the field of qualitative enquiry, its potential usefulness in nutrition and dietetics, and how to embark upon this type of research. Furthermore, it describes a process to guide high‐quality qualitative research in this area that proceeds from the research question(s) and considers the key philosophical assumptions about ontology, epistemology and methodology that underpin the overall design of a study. Other reviews in this series provide an overview of the principal techniques of data collection and sampling, data analysis, and quality assessment of qualitative work, and provide some practical advice relevant to nutrition and dietetics, along with glossaries of key terms.
Signal peptide‐regulated toxicity of a plant ribosome‐inactivating protein during cell stress
Authors: Marshall Richard S. , D’Avila Francesca , Di Cola Alessandra , Traini Roberta , Spanò Laura , Fabbrini Maria Serena , Ceriotti Aldo 
Published: October 2010

SummaryThe fate of the type I ribosome‐inactivating protein (RIP) saporin when initially targeted to the endoplasmic reticulum (ER) in tobacco protoplasts has been examined. We find that saporin expression causes a marked decrease in protein synthesis, indicating that a fraction of the toxin reaches the cytosol and inactivates tobacco ribosomes. We determined that saporin is largely secreted but some is retained intracellularly, most likely in a vacuolar compartment, thus behaving very differently from the prototype RIP ricin A chain. We also find that the signal peptide can interfere with the catalytic activity of saporin when the protein fails to be targeted to the ER membrane, and that saporin toxicity undergoes signal sequence‐specific regulation when the host cell is subjected to ER stress. Replacement of the saporin signal peptide with that of the ER chaperone BiP reduces saporin toxicity and makes it independent of cell stress. We propose that this stress‐induced toxicity may have a role in pathogen defence.
Identification of legume RopGEF gene families and characterization of a Medicago truncatula RopGEF mediating polar growth of root hairs
Authors: Riely Brendan K. , He Hengbin , Venkateshwaran Muthusubramanian , Sarma Birinchi , Schraiber Joshua , Ané Jean‐Michel , Cook Douglas R. 
Published: October 2010

SummaryRoot hairs play important roles in the interaction of plants with their environment. Root hairs anchor the plant in the soil, facilitate nutrient uptake from the rhizosphere, and participate in symbiotic plant–microbe interactions. These specialized cells grow in a polar fashion which gives rise to their elongated shape, a process mediated in part by a family of small GTPases known as Rops. RopGEFs (GEF, guanine nucleotide exchange factor) activate Rops to effect tip growth in Arabidopsis pollen and root hairs, but the genes mediating tip growth in legumes have not yet been characterized. In this report we describe the Rop and RopGEF gene families from the model legume Medicago truncatula and from the crop legume soybean. We find that one member of the M. truncatula gene family, MtRopGEF2, is required for root hair development because silencing this gene by RNA interference affects the cytosolic Ca2+ gradient and subcellular structure of root hairs, and reduces root hair growth. Consistent with its role in polar growth, we find that a GFP::MtRopGEF2 fusion protein localizes in the apex of emerging and actively growing root hairs. The amino terminus of MtRopGEF2 regulates its ability to interact with MtRops in yeast, and regulates its biological activity in vivo.
Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula
Authors: Murray Jeremy D. , Muni RajaSekhara Reddy Duvvuru , Torres‐Jerez Ivone , Tang Yuhong , Allen Stacy , Andriankaja Megan , Li Guangming , Laxmi Ashverya , Cheng Xiaofei , Wen Jiangqi , Vaughan David , Schultze Michael , Sun Jongho , Charpentier Myriam , Oldroyd Giles , Tadege Million , Ratet Pascal , Mysore Kirankumar S. , Chen Rujin , Udvardi Michael K. 
Published: October 2010

SummaryIntracellular invasion of root cells is required for the establishment of successful endosymbioses in legumes of both arbuscular mycorrhizal (AM) fungi and rhizobial bacteria. In both interactions a requirement for successful entry is the activation of a common signalling pathway that includes five genes required to generate calcium oscillations and two genes required for the perception of the calcium response. Recently, it has been discovered that in Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Here, we show by analyses of mutants that the same gene is also required for rhizobial colonization and nodulation. VPY encodes a protein featuring a Major Sperm Protein domain, typically featured on proteins involved in membrane trafficking and biogenesis, and a series of ankyrin repeats. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. Calcium spiking in root hairs in response to supplied Nod factors is intact in the vpy‐1 mutant. This, and the elevation of VPY transcripts upon application of Nod factors which we show to be dependent on NFP, DMI1, and DMI3, indicates that VPY acts downstream of the common signalling pathway.
OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment
Authors: Park Jong‐Jin , Yi Jakyung , Yoon Jinmi , Cho Lae‐Hyeon , Ping Jin , Jeong Hee Joong , Cho Seok Keun , Kim Woo Taek , An Gynheung 
Published: October 2010

SummaryThe plant U‐box (PUB) protein functions as an E3 ligase to poly‐ubiquitinate a target protein for its degradation or post‐translational modification. Here, we report functional roles for OsPUB15, which encodes a cytosolic U‐box protein in the class‐II PUB family. Self‐ubiquitination assays showed that bacterially expressed MBP‐OsPUB15 protein has E3 ubiquitin ligase activity. A T‐DNA insertional mutation in OsPUB15 caused severe growth retardation and a seedling‐lethal phenotype. Mutant seeds did not produce primary roots, and their shoot development was significantly delayed. Transgenic plants expressing the OsPUB15 antisense transcript phenocopied these mutant characters. The abnormal phenotypes were partially rescued by two antioxidants, catechin and ascorbic acid. Germinating seeds in the dark also recovered the rootless defect. Levels of H2O2 and oxidized proteins were higher in the knock‐out mutant compared with the wild type. OsPUB15 transcript levels were increased upon H2O2, salt and drought stresses; plants overexpressing the gene grew better than the wild type under high salinity. These results indicate that PUB15 is a regulator that reduces reactive oxygen species (ROS) stress and cell death.
Measurement of cellular cGMP in plant cells and tissues using the endogenous fluorescent reporter FlincG
Authors: Isner Jean‐Charles , Maathuis Frans J. M. 
Published: October 2010

SummaryThe cyclic nucleotide cGMP has been shown to play important roles in plant development and responses to abiotic and biotic stress. To date, the techniques that are available to measure cGMP in plants are limited by low spatial and temporal resolution. In addition, tissue destruction is necessary. To circumvent these drawbacks we have used the δ‐FlincG fluorescent protein to create an endogenous cGMP sensor that can report cellular cGMP levels with high resolution in time and space in living plant cells. δ‐FlincG in transient and stably expressing cells shows a dissociation constant for cGMP of around 200 nm giving it a dynamic range of around 20–2000 nm. Stimuli that were previously shown to alter cGMP in plant cells (nitric oxide and gibberrellic acid) evoked pronounced fluorescence signals in single cells and in root tissues, providing evidence that δ‐FlincG reports changes in cellular cGMP in a physiologically relevant context.
Dorsal hippocampal opioidergic system modulates anxiety‐like behaviors in adult male Wistar rats
Authors: Solati Jalal , Zarrindast Mohammad‐Reza , Salari Ali‐Akbar 
Published: October 2010

Aims: In the present study, we investigated the possible influence of the opioidergic system of the dorsal hippocampus on anxiety‐like behaviors.Methods: Elevated plus‐maze, which is one of the methods used for testing anxiety, was used in the present study. Rats were anesthetized with ketamine and xylazine and special cannulas were inserted stereotaxically into the CA1 region of the dorsal hippocampus. After 1 week of recovery, the effects of intra‐CA1 administration of morphine (0.25, 0.5, 1 and 2 µg/rat; 1 µl/rat; 0.5 µl/in each side), naloxone (2, 4, 6 and 8 µg/rat), enkephalin (1, 2, 5 and 10 µg/rat) and naltrindole (0.25, 0.5, 1 and 2 µg/rat) on percentage open arm time (%OAT) and percentage open arm entries (%OAE) were determined.Results: Bilateral administration of morphine into CA1 decreases %OAT and %OAE, indicating an anxiogenic‐like effect. Intra‐CA1 injection of naloxone, an opioid receptor antagonist, increased both %OAT and %OAE, parameters of anxiolytic‐like behavior. Bilateral administration of δ‐opioid receptor agonist, [D‐Pen2,5]‐enkephalin acetate hydrate into the CA1, induced an anxiolytic‐like effect. Furthermore, intra‐CA1 injection of δ‐opioid receptor antagonist, naltrindole hydrochloride, increased anxiety‐related behaviors.Conclusions: The results of the present study demonstrate that activation of μ‐opioid receptors in this area produce an anxiogenic response while activation of δ‐opioid receptors produces an anxiolytic response.
Serum ghrelin is inversely associated with cognitive function in a sample of non‐demented elderly
Authors: Spitznagel Mary Beth , Benitez Andreana , Updegraff John , Potter Vanessa , Alexander Thomas , Glickman Ellen , Gunstad John 
Published: October 2010

Aim:  The orexigenic hormone, ghrelin, is linked to learning and memory in animal studies. No previous study has investigated whether cognition is related to ghrelin in the non‐demented elderly.Methods:  Thirty‐five older adults underwent neuropsychological testing and fasting blood draw with subsequent serum ghrelin quantification.Results:  Ghrelin was negatively correlated with several cognitive domains, including verbal memory, working memory, and naming.Conclusion:  Areas of cognition associated with ghrelin level were similar to the pattern of deficits observed in early Alzheimer's disease. Findings suggest a potential moderational role of ghrelin in pathological cognitive decline. Further work investigating mechanisms is needed.
From body‐talk to body‐stories: body work in complementary and alternative medicine
Authors: Gale Nicola Kay 
Published: October 2010

AbstractThis paper explores the ‘body work’ undertaken by practitioners of complementary and alternative medicine (CAM), in the light of ethnographic research on the education of osteopaths and homeopaths. The data presented focus on practitioners’ experiences of learning to communicate, touch and facilitate the healing process for their patients. Two new concepts are introduced: listening to body‐talk and constructing body‐stories, which are discussed as aspects of body work. Body‐talk expresses the idea that the embodied patient is not a passive recipient of healthcare, but that the ‘body’ is able to communicate its distress and its needs. The body‐story concept highlights the interactional nature of the therapeutic encounter and the profound interrelation between the treatment and case‐taking aspects of the practitioner’s clinical tasks. By drawing on key sociological concepts of the body and embodiment, reflexivity and narrative, I argue that the dialogical construction of body‐stories challenges Cartesian dualism. Finally, I discuss what the data might mean for the future development of the sociological concept of ‘body work’, drawing particular attention to the necessity to problematise the concept of the ‘body’ and to pay great attention to body work as embodied work.
Do Hospitals Alter Patient Care Effort Allocations under Pay‐for‐Performance?
Authors: Nicholas Lauren Hersch , Dimick Justin B. , Iwashyna Theodore J. 
Published: October 2010

Objective. To determine whether hospitals increase efforts on easy tasks relative to difficult tasks to improve scores under pay‐for‐performance (P4P) incentives.Data Source. The Centers for Medicare and Medicaid Services Hospital Compare data from Fiscal Years 2003 through 2005 and 2003 American Hospital Association Annual Survey data.Study Design. We classified measures of process compliance targeted by the Premier Hospital Quality Incentive Demonstration as easy or difficult to improve based on whether they introduce additional per‐patient costs. We compared process compliance on easy and difficult tasks at hospitals eligible for P4P bonus payments relative to hospitals engaged in public reporting using random effects regression models.Principal Findings. P4P hospitals did not preferentially increase efforts for easy tasks in patients with heart failure or pneumonia, but they did exhibit modestly greater effort on easy tasks for heart attack admissions. There is no systematic evidence that effort was allocated toward easier processes of care and away from more difficult tasks.Conclusions. Despite perverse P4P incentives to change allocation of efforts across tasks to maximize performance scores at lowest cost, we find little evidence that hospitals respond to P4P incentives as hypothesized. Alternative incentive structures may motivate greater response by targeted hospitals.