bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated transcriptomic and proteomic profiling of white spruce stems during the transition from active growth to dormancy
Authors: GALINDO GONZÁLEZ LEONARDO M. , EL KAYAL WALID , JU CHELSEA J.‐T. , ALLEN CARMEN C. G. , KING‐JONES SUSANNE , COOKE JANICE E. K. 
Published: October 2011

ABSTRACTIn the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth‐to‐dormancy transition in a conifer, white spruce (Picea glauca[Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree's overwintering preparations. For example, genes associated with carbon‐based defences such as terpenoids were down‐regulated, while many genes associated with protein‐based defences and other stress mitigation mechanisms were up‐regulated. Several of these correspond to proteins that were accumulated during the growth‐to‐dormancy transition, emphasizing the importance of stress protection in the tree's adaptive response to overwintering.
Different Effects of Bortezomib on the Expressions of Various Protein Kinase C Isoenzymes in T Cells of Patients with Systemic Lupus Erythematosus and in Jurkat Cells
Authors: Griger Z. , Tóth B. I. , Baráth S. , Gyetvai Á. , Kovács I. , Tarr T. , Bíró T. , Zeher M. , Sipka S. 
Published: October 2011

AbstractThe effects of proteosome inhibitor Bortezomib (BZ) were studied in vitro for 24 h on the protein kinase C (PKC) profiles, rates of proliferation and apoptosis in Jurkat cells and lymphocytes of 10 patients with systemic lupus erythematosus (SLE) and nine healthy subjects. The expressions of PKC proteins, the rates of proliferation and apoptosis were determined. The effects of BZ were different in the Jurkat and lupus T cells. Whereas BZ elevated the expression of PKC θ, δ and ξ isoenzymes in the Jurkat cells, it was unable to do that in the lupus T cells. BZ induced a dose‐dependent increase in the apoptosis of Jurkat cells, while decreased the proliferation. The same effect of BZ was observed on the apoptosis of lymphocytes both in SLE and healthy subjects at concentrations higher than the therapeutic dose. We conclude that BZ treatment in vitro was not able to restore the SLE‐specific defect (decrease) in the expression of PKC isoenzymes in the T cells as it was expected. This can be a limiting factor in the positive clinical effects of BZ in lupus.
River‐dominated, shelf‐edge deltas: delivery of sand across the shelf break in the absence of slope incision
Authors: DIXON JOSHUA F , STEEL RONALD J , OLARIU CORNEL 
Published: October 2011

AbstractShelf‐edge deltas record the potential magnitude of sediment delivery from shallow water shelf into deep water slope and basin floor and, if un‐incised, represent the main increment of shelf‐margin growth into the basin, for that period. The three‐dimensional complexity of shelf‐edge delta systems and along‐strike variability at the shelf edge in particular, remains understudied. The Permian–Triassic Kookfontein Formation of the Tanqua Karoo Basin, South Africa, offers extensive three‐dimensional exposure (>100 km2) and therefore a unique opportunity to evaluate shelf‐edge strata from an outcrop perspective. Analysis of stratal geometry and facies distribution from 52 measured and correlated stratigraphic sections show the following: (i) In outer‐shelf areas, parasequences are characterized by undeformed, river‐dominated, storm‐wave influenced delta mouth‐bar sandstones interbedded with packages showing evidence of syn‐depositional deformation. The amount and intensity of soft‐sediment deformation increases significantly towards the shelf edge where slump units and debris flows sourced from collapsed mouth‐bar packages transport material down slope. (ii) On the upper slope, mouth‐bar and delta‐front sandstones pinch out within 2 km of the shelf break and most slump and debris flow units pinch out within 4 km of the shelf break. (iii) Further down the slope, parasequences consist of finer‐grained turbidites, characterized by interbedded, thin tabular siltstones and sandstones. The results highlight that river‐dominated, shelf‐edge deltas transport large volumes of sand to the upper slope, even when major shelf‐edge incisions are absent. In this case, transport to the upper slope through slumping, debris flows and un‐channellized low density turbidites is distributed evenly along strike.
Ichnology and sedimentology of the Triassic carbonates of North‐west Sardinia, Italy
Authors: KNAUST DIRK , COSTAMAGNA LUCA G. 
Published: October 2011

AbstractThe classical Middle to Upper Triassic carbonate sections at Monte Santa Giusta and Punta del Lavatoio, North‐west Sardinia (Italy), referred to the Muschelkalk and Keuper lithofacies group, are revisited and their trace fossil content is investigated for the first time. A combined ichnological and sedimentological study reveals insights into the depositional environments, regional context, palaeogeography and sequence stratigraphy. The results indicate deposition on a homoclinal carbonate ramp with broad facies belts. All recognized trace fossils are also known from time‐equivalent deposits of Germany and thus indicate a close affinity between the North‐west Sardinian Triassic and the Germanic Basin. Only a few trace fossils are particularly abundant and these indicate opportunistic colonization by their producers, which is probably related to restricted endobenthic conditions due to reduced oxygen and/or increased salinity. The trace fossil association can be grouped into a softground suite belonging to the Cruziana ichnofacies, and a firmground suite of the Glossifungites ichnofacies. This discrimination enables an interpretation of the northern Monte Santa Giusta section as a carbonate ramp with extensive tidal flats and abundant carbonate accumulation in a relatively proximal position, whereas the southern Punta del Lavatoio section exhibits broad lagoonal environments with reduced sedimentation in a deeper and more Tethys‐influenced area. The Sardinian sections are ichnologically similar to the Anisian–Ladinian succession known from the Tatra Mountains, but differ from it by having a slightly higher ichnodiversity, which again can be attributed to a less restricted lagoonal environment. This study demonstrates the importance of integrating trace fossil analysis in sedimentological and palaeontological investigations of carbonate systems.
The human P2X7 receptor and its role in innate immunity
Authors: Wiley J. S. , Sluyter R. , Gu B. J. , Stokes L. , Fuller S. J. 
Published: October 2011

The human P2X7 receptor is a two‐transmembrane ionotropic receptor which has a ubiquitous distribution and is most highly expressed on immune cells. In macrophages and similar myeloid cells primed by lipopolysaccharide (LPS), activation of P2X7 by extracellular ATP opens a cation channel/pore allowing massive K+ efflux associated with processing and secretion of pro‐inflammatory cytokines interleukin (IL)‐1β and IL‐18. A variety of other downstream effects follows P2X7 activation over several minutes including shedding of certain surface molecules, membrane blebbing, microvesicle/exosome release and apoptosis of the cell. High concentrations of ATP (>100 µM) are required to activate P2X7 but it remains unclear where these levels exist, other than in inflammatory foci or confined spaces such as in bone. A variety of potent selective antagonists of P2X7 activation have recently become available, allowing clinical trials to be undertaken in inflammatory and immune‐mediated disorders.Proteomic studies have shown that P2X7 exists as a large multiprotein complex which includes non‐muscle myosin heavy chain and other elements of the cytoskeleton. In the absence of its ATP ligand and serum, P2X7 has an alternate function in the recognition and phagocytosis of non‐opsonized foreign particles, including bacteria and apoptotic cells. The P2RX7 gene has many polymorphic variants and isoforms which increase or decrease function of the receptor. Genetic association studies have linked loss‐of‐function polymorphisms with reactivation of latent tuberculosis as well as symptomatic infection with certain other obligate intracellular pathogens. The many roles involving P2X7 suggest that this receptor is essential to fundamental aspects of the innate immune response.
Dexamethasone has additive effect when combined with ondansetron and droperidol for treatment of established PONV
Authors: ORMEL G. , ROMUNDSTAD L. , LAMBERT‐JENSEN P. , STUBHAUG A. 
Published: October 2011

BackgroundProphylactic dexamethasone, ondansetron and droperidol have a documented effect on post‐operative nausea and vomiting (PONV). Still, there is a lack of studies investigating the effect of adding dexamethasone to ondansetron and droperidol in order to treat established PONV.MethodsIn this double‐blind randomised, controlled trial, we compared triple prophylaxis for PONV consisting of dexamethasone 8 mg intravenous (IV), ondansetron 4 mg IV and droperidol 0.625 mg IV (n = 157) with placebo (n = 156) given before gynaecological day‐case surgery. Subsequently, in those having PONV despite triple prophylaxis or placebo, a dose of ondansetron and droperidol plus dexamethasone was compared with the combination of ondansetron and droperidol.ResultsTriple prophylaxis reduced acute PONV (0–6 h) (P = 0.0003) and post‐discharge PONV (6–24 h) (P = 0.001) when compared with placebo. Among those suffering from PONV despite placebo or active prophylaxis (n = 80), adding dexamethasone to ondansetron and droperidol reduced acute PONV (0–6 h) (P = 0.025) as well as post‐discharge nausea (6–24 h) (P = 0.04) compared with duo treatment comprising ondansetron and droperidol. In those reporting PONV despite prophylaxis (n = 12), the treatment comprising ondansetron and droperidol, with or without dexamethasone, gave a 91.7% reduction in acute PONV and an 83.6% reduction in post‐discharge PONV.ConclusionTreatment of established PONV comprising ondansetron and droperidol, with or without dexamethasone, reduced PONV in both treatment groups. In those reporting PONV without active prophylaxis, the addition of dexamethasone resulted in a significant amplification of the PONV, reducing effects of ondansetron and droperidol.
A mass mortality of subtropical intertidal populations of the sea urchin Paracentrotus lividus: analysis of potential links with environmental conditions
Authors: Girard Dominique , Clemente Sabrina , Toledo‐Guedes Kilian , Brito Alberto , Hernández José Carlos 
Published: October 2011

AbstractAn outbreak of bald sea urchin disease was detected affecting intertidal populations of the edible temperate species Paracentrotus lividus at its southernmost geographical limit. The mortality event was detected in three sites (Güímar, Palmar and Alcalá) off Tenerife, Canary Islands (Northeastern Atlantic), in October 2003, coinciding with the highest sea surface temperatures (SST) and the lowest wave heights of the year. The prevalence of infection reached 100% but did not affect equally all studied sites or the different size classes. The disease was more prevalent in large sea urchins (>40 mm). The prevalence appeared to be positively correlated with the environmental variable SST and negatively correlated with wave height. In October 2004, only two infected urchins were found (prevalence 1%) at one of the studied sites. However, during 2004 no such extreme values of temperature and wave height were observed. We conclude that high SSTs and low wave heights such as those observed during 2003 are conditions that may trigger outbreaks of urchin disease.
Effectiveness of fast‐track rehabilitation vs conventional care in laparoscopic colorectal resection for elderly patients: a randomized trial
Authors: Wang Q. , Suo J. , Jiang J. , Wang C. , Zhao Y.‐Q. , Cao X. 
Published: October 2011

AbstractAim  The aim of the study was to evaluate the efficacy and safety of fast‐track rehabilitation in elderly patients over 65 years of age, following laparoscopic surgery to remove colorectal cancer.Method  A total of 78 elderly patients with colorectal cancer who underwent laparoscopic colorectal resection were randomly assigned to receive either the fast‐track care programme (n = 40) or the conventional perioperative care protocol (control group, n = 38). Medical personnel conducting the study were blinded to patients’ clinical outcomes prior to statistical analysis. The fast‐track protocol included no preoperative mechanical bowel irrigation, immediate oral alimentation and earlier postoperative ambulation exercise. The length of postoperative hospital stay, the length of time to regain bowel function and the rate of postoperative complications were compared between the two groups.Results  The length of time to regain bowel function, including the passage of flatus[31 (26–40) h vs 38 (32–51) h, P = 0.001], to the first bowel movement [55 (48–63) h vs 64 (48–71) h, P = 0.009] and to start a liquid diet (12 [11–16] h vs 47 [35–50] h, P = 0.000) were significantly shorter in patients receiving the fast‐track care protocol compared with those receiving the conventional care protocol. A shorter duration of postoperative hospital stay was recorded in patients receiving the fast‐track program than in those receiving conventional care (P = 0.0001). A reduced percentage of patients who developed general complications was also observed in the fast‐track group (5.0%vs 21.1%, P = 0.045).Conclusion  This randomized controlled trial has shown that in the elderly undergoing laparoscopic colorectal surgery, the fast‐track recovery programme resulted in a more rapid postoperative recovery, earlier discharge from hospital and fewer general complications compared with a conventional postoperative protocol.
Modeling Alternative Sequences of Events in Dynamic Geographic Domains
Authors: Hubbard Shane , Hornsby Kathleen Stewart 
Published: October 2011

AbstractA model that emphasizes possible alternative sequences of events that occur over time is presented in this article. Representing alternative orbranching eventscaptures additional semantics unrealized by linear or non‐branching approaches. Two basic elements of branching,divergenceandconvergenceare discussed. From these elements, many complex branching models can be built capturing a perspective of events that will take place in the future or have occurred in the past. This produces likely sequences of events that a user may compare and analyze using spatial or temporal criteria. The branching events model is especially useful for spatiotemporal decision support systems, as decision‐makers are able to identify alternative locations and times of events and, depending on the context, also identify regions of multiple possible events. A branching events viewer application is presented illustrating a case study based on a tornado response.
Using Federated Catalogs to Improve Semantic Integration among Spatial Data Infrastructures
Authors: de Andrade Fabio Gomes , Baptista Cláudio de Souza , Leite Jr Fabio Luiz 
Published: October 2011

AbstractNowadays, Spatial Data Infrastructures (SDIs) play an important role in government agencies, at different levels: global, national, and local. They aim to improve the management and sharing of geospatial data. Nonetheless, these SDIs have been developed as information islands, in which a user's query is compared to metadata described only in their own catalog services. The lack of interaction among SDIs limits the potential of these infrastructures in providing geospatial data to a larger audience. This article presents a distributed architecture, based on a federation of SDIs which interact among themselves, using query propagation. This propagation facilitates data discovery and sharing. We also describe a distributed query processing service used to enable the resource discovery in distributed infrastructures.
LINKAGES BETWEEN EXCHANGE RATE POLICY AND MACROECONOMIC PERFORMANCE
Authors: SOKOLOV VLADIMIR , LEE BYUNG‐JOO , MARK NELSON C. 
Published: October 2011

AbstractUsing a sample of 104 countries, we study macroeconomic performance from 1973 to 2007. We examine GDP growth, inflation rate, growth volatility and inflation volatility, and their response to a ‘words versus deeds’ measure of exchange‐rate policy, which is obtained by interacting a country's de jure and its de facto policy. For non‐industrialized countries, the highest growth rates and the lowest inflation volatility are associated with countries that pursue fear of floating policy, whereas countries that pursue a matched float policy (de jure and de facto floating) have the highest inflation rates but the lowest GDP volatility.
‘MENTAL HEALTH AND EMPLOYMENT OF THE ELDERLY IN TAIWAN: A SIMULTANEOUS EQUATION APPROACH
Authors: CHANG HUNG‐HAO , YEN STEVEN T. 
Published: October 2011

AbstractLonger life expectancy and declining birth rates have contributed to an aging population in many countries. This paper addresses the relationship between mental health and employment status among the elderly in Taiwan. A simultaneous equation system is developed that accommodates the discrete and censored nature of the two endogenous variables. Using data from a nationwide survey of the elderly in Taiwan, we find that older adults with mental illness are less likely to work, while those currently working are less prone to mental illness compared to their unemployed cohort.
From embryo sac to oil and protein bodies: embryo development in the model legume Medicago truncatula
Authors: Wang Xin‐Ding , Song Youhong , Sheahan Michael B. , Garg Manohar L. , Rose Ray J. 
Published: October 2011

Summary
The cell and developmental biology of zygotic embryogenesis in the model legume Medicago truncatula has received little attention. We studied M. truncatula embryogenesis from embryo sac until cotyledon maturation, including oil and protein body biogenesis.
We characterized embryo development using light and electron microscopy, measurement of protein and lipid fatty acid accumulation and by profiling the expression of key seed storage genes.
Embryo sac development in M. truncatula is of the Polygonum type. A distinctive multicellular hypophysis and suspensor develops before the globular stage and by the early cotyledon stage, the procambium connects the developing apical meristems. In the storage parenchyma of cotyledons, ovoid oil bodies surround protein bodies and the plasma membrane. Four major lipid fatty acids accumulate as cotyledons develop, paralleling the expression of OLEOSIN and the storage protein genes, VICILIN and LEGUMIN.
Zygotic embryogenesis in M. truncatula features the development of a distinctive multicellular hypophysis and an endopolyploid suspensor with basal transfer cell. A clear procambial connection between the apical meristems is evident and there is a characteristic arrangement of oil bodies in the cotyledons and radicle. Our data help link embryogenesis to the genetic regulation of oil and protein body biogenesis in legume seed.
Repairing breaks in the plant genome: the importance of keeping it together
Authors: Waterworth Wanda M. , Drury Georgina E. , Bray Clifford M. , West Christopher E. 
Published: October 2011

SummaryDNA damage threatens the integrity of the genome and has potentially lethal consequences for the organism. Plant DNA is under continuous assault from endogenous and environmental factors and effective detection and repair of DNA damage are essential to ensure the stability of the genome. One of the most cytotoxic forms of DNA damage are DNA double‐strand breaks (DSBs) which fragment chromosomes. Failure to repair DSBs results in loss of large amounts of genetic information which, following cell division, severely compromises daughter cells that receive fragmented chromosomes. This review will survey recent advances in our understanding of plant responses to chromosomal breaks, including the sources of DNA damage, the detection and signalling of DSBs, mechanisms of DSB repair, the role of chromatin structure in repair, DNA damage signalling and the link between plant recombination pathways and transgene integration. These mechanisms are of critical importance for maintenance of plant genome stability and integrity under stress conditions and provide potential targets for the improvement of crop plants both for stress resistance and for increased precision in the generation of genetically improved varieties.

Contents

Summary
805

I.
Introduction
806

II.
Sources of DNA damage
806

III.
The toxic effects of DSBs
806

IV.
Detection of DSBs
806

V.
Growth responses to genotoxic stress
809

VI.
Chromatin structure and DSB repair
810

VII.
Genome stability and environmental stress
811

VIII.
Mechanisms of DSB repair
813

IX.
Outlook
818

Acknowledgements
818

References
818
The phosphorylation status of extracellular‐regulated kinase 1/2 in astrocytes and neurons from rat hippocampus determines the thrombin‐induced calcium release and ROS generation
Authors: Zündorf Gregor , Reiser Georg 
Published: October 2011

J. Neurochem. (2011) 10.1111/j.1471‐4159.2011.07527.xAbstractChallenge of protease‐activated receptors induces cytosolic Ca2+ concentration ([Ca2+]c) increase, mitogen‐activated protein kinase activation and reactive oxygen species (ROS) formation with a bandwidth of responses in individual cells. We detected in this study in situ the thrombin‐induced [Ca2+]c rise and ROS formation in dissociated hippocampal astrocytes and neurons in a mixed culture. In identified cells, single cell responses were correlated with extracellular‐regulated kinase (ERK)1/2 phosphorylation level. On average, in astrocytes, thrombin induced a transient [Ca2+]c rise with concentration‐dependent increase in amplitude and extrusion rate and high ERK1/2 phosphorylation level. Correlation analysis of [Ca2+]c response characteristics of single astrocytes reveals that astrocytes with nuclear phosphoERK1/2 localization have a smaller Ca2+amplitude and extrusion rate compared with cells with a cytosolic phosphoERK1/2 localization. In naive neurons, without thrombin challenge, variable ERK1/2 phosphorylation patterns are observed. ROS were detected by hydroethidine. Only in neurons with increased ERK1/2 phosphorylation level, we see sustained intracellular rise in fluorescence of the dye lasting over several minutes. ROS formation was abolished by pre‐incubation with the NADPH oxidase inhibitor apocynin. Additionally, thrombin induced an immediate, transient hydroethidine fluorescence increase. This was interpreted as NADPH oxidase‐mediated O2•−‐release into the extracellular milieu, because it was decreased by pre‐incubation with apocynin, and could be eluted by superfusion. In conclusion, the phosphorylation status of ERK1/2 determines the thrombin‐dependent [Ca2+]c increase and ROS formation and, thus, influences the capacity of thrombin to regulate neuroprotection or neurodegeneration.