bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Global View of Non-Gaussian SST Variability
Authors: Sura Philip , Sardeshmukh Prashant D. 
Published: March 2008

Abstract
The skewness and kurtosis of daily sea surface temperature (SST) variations are found to be strongly linked at most locations around the globe in a new high-resolution observational dataset, and are analyzed in terms of a simple stochastically forced mixed layer ocean model. The predictions of the analytic theory are in remarkably good agreement with observations, strongly suggesting that a univariate linear model of daily SST variations with a mixture of SST-independent (additive) and SST-dependent (multiplicative) noise forcing is sufficient to account for the skewness–kurtosis link. Such a model of non-Gaussian SST dynamics should be useful in predicting the likelihood of extreme events in climate, as many important weather and climate phenomena, such as hurricanes, ENSO, and the North Atlantic Oscillation (NAO), depend on a detailed knowledge of the underlying local SSTs.
Nonnormal Thermohaline Circulation Dynamics in a Coupled Ocean–Atmosphere GCM
Authors: Tziperman Eli , Zanna Laure , Penland Cecile 
Published: March 2008

Abstract
Using the GFDL coupled atmosphere–ocean general circulation model CM2.1, the transient amplification of thermohaline circulation (THC) anomalies due to its nonnormal dynamics is studied. A reduced space based on empirical orthogonal functions (EOFs) of temperature and salinity anomaly fields in the North Atlantic is constructed. Under the assumption that the dynamics of this reduced space is linear, the propagator of the system is then evaluated and the transient growth of THC anomalies analyzed. Although the linear dynamics are stable, such that any initial perturbation eventually decays, nonnormal effects are found to result in a significant transient growth of temperature, salinity, and THC anomalies. The growth time scale for these anomalies is between 5 and 10 yr, providing an estimate of the predictability time of the North Atlantic THC in this model. There are indications that these results are merely a lower bound on the nonnormality of THC dynamics in the present coupled GCM. This seems to suggest that such nonnormal effects should be seriously considered if the predictability of the THC is to be quantitatively evaluated from models or observations. The methodology presented here may be used to produce initial perturbations to the ocean state that may result in a stricter estimate of ocean and THC predictability than the common procedure of initializing with an identical ocean state and a perturbed atmosphere.
Winter Eddy Genesis in the Eastern South China Sea due to Orographic Wind Jets
Authors: Wang Guihua , Chen Dake , Su Jilan 
Published: March 2008

Abstract
Generation of mesoscale eddies in the eastern South China Sea (SCS) in winters during August 1999 to July 2002 is studied with a reduced-gravity model. It is found that the orographic wind jets associated with the northeast winter monsoon and the gaps in the mountainous island chain along the eastern boundary of the SCS can spin up cyclonic and anticyclonic eddies over the SCS. Results suggest that direct wind forcing could be an important generation mechanism for the rich eddy activity in the SCS, and that to simulate this mechanism the resolution of the wind forcing has to be high enough to resolve the local wind jets induced by orographic effects.
Aquaplanets, Climate Sensitivity, and Low Clouds
Authors: Medeiros Brian , Stevens Bjorn , Held Isaac M. , Zhao Ming , Williamson David L. , Olson Jerry G. , Bretherton Christopher S. 
Published: March 2008

Abstract
Cloud effects have repeatedly been pointed out as the leading source of uncertainty in projections of future climate, yet clouds remain poorly understood and simulated in climate models. Aquaplanets provide a simplified framework for comparing and understanding cloud effects, and how they are partitioned as a function of regime, in large-scale models. This work uses two climate models to demonstrate that aquaplanets can successfully predict a climate model’s sensitivity to an idealized climate change. For both models, aquaplanet climate sensitivity is similar to that of the realistic configuration. Tropical low clouds appear to play a leading role in determining the sensitivity. Regions of large-scale subsidence, which cover much of the tropics, are most directly responsible for the differences between the models. Although cloud effects and climate sensitivity are similar for aquaplanets and realistic configurations, the aquaplanets lack persistent stratocumulus in the tropical atmosphere. This, and an additional analysis of the cloud response in the realistically configured simulations, suggests the representation of shallow (trade wind) cumulus convection, which is ubiquitous in the tropics, is largely responsible for differences in the simulated climate sensitivity of these two models.
Long-term Air Pollution Exposure Is Associated with Neuroinflammation, an Altered Innate Immune Response, Disruption of the Blood-Brain Barrier, Ultrafine Particulate Deposition, and Accumulation of Amyloid β-42 and α-Synuclein in Children and Young Adults
Authors: Calderón-Garcidueñas Lilian , Solt Anna C. , Henríquez-Roldán Carlos , Torres-Jardón Ricardo , Nuse Bryan , Herritt Lou , Villarreal-Calderón Rafael , Osnaya Norma , Stone Ida , García Raquel , Brooks Diane M. , González-Maciel Angelica , Reynoso-Robles Rafael , Delgado-Chávez Ricardo , Reed William 
Published: March 2008

Air pollution is a serious environmental problem. We investigated whether residency in cities with high air pollution is associated with neuroinflammation/neurodegeneration in healthy children and young adults who died suddenly. We measured mRNA cyclooxygenase-2, interleukin-1β, and CD14 in target brain regions from low (n = 12) or highly exposed residents (n = 35) aged 25.1 ± 1.5 years. Upregulation of cyclooxygenase-2, interleukin-1β, and CD14 in olfactory bulb, frontal cortex, substantia nigrae and vagus nerves; disruption of the blood-brain barrier; endothelial activation, oxidative stress, and inflammatory cell trafficking were seen in highly exposed subjects. Amyloid β42 (Aβ42) immunoreactivity was observed in 58.8% of apolipoprotein E (APOE) 3/3 < 25 y, and 100% of the APOE 4 subjects, whereas α-synuclein was seen in 23.5% of < 25 y subjects. Particulate material (PM) was seen in olfactory bulb neurons, and PM < 100 nm were observed in intraluminal erythrocytes from lung, frontal, and trigeminal ganglia capillaries. Exposure to air pollution causes neuroinflammation, an altered brain innate immune response, and accumulation of Aβ42 and α-synuclein starting in childhood. Exposure to air pollution should be considered a risk factor for Alzheimer’s and Parkinson’s diseases, and carriers of the APOE 4 allele could have a higher risk of developing Alzheimer’s disease if they reside in a polluted environment.
Anacardic acid (6-nonadecyl salicylic acid), an inhibitor of histone acetyltransferase, suppresses expression of nuclear factor-κB–regulated gene products involved in cell survival, proliferation, invasion, and inflammation through inhibition of the inhibitory subunit of nuclear factor-κBα kinase, leading to potentiation of apoptosis
Authors: Sung Bokyung , Pandey Manoj K. , Ahn Kwang Seok , Yi Tingfang , Chaturvedi Madan M. , Liu Mingyao , Aggarwal Bharat B. 
Published: March 2008

AbstractAnacardic acid (6-pentadecylsalicylic acid) is derived from traditional medicinal plants, such as cashew nuts, and has been linked to anticancer, anti-inflammatory, and radiosensitization activities through a mechanism that is not yet fully understood. Because of the role of nuclear factor-κB (NF-κB) activation in these cellular responses, we postulated that anacardic acid might interfere with this pathway. We found that this salicylic acid potentiated the apoptosis induced by cytokine and chemotherapeutic agents, which correlated with the down-regulation of various gene products that mediate proliferation (cyclin D1 and cyclooxygenase-2), survival (Bcl-2, Bcl-xL, cFLIP, cIAP-1, and survivin), invasion (matrix metalloproteinase-9 and intercellular adhesion molecule-1), and angiogenesis (vascular endothelial growth factor), all known to be regulated by the NF-κB. We found that anacardic acid inhibited both inducible and constitutive NF-κB activation; suppressed the activation of IκBα kinase that led to abrogation of phosphorylation and degradation of IκBα; inhibited acetylation and nuclear translocation of p65; and suppressed NF-κB–dependent reporter gene expression. Down-regulation of the p300 histone acetyltransferase gene by RNA interference abrogated the effect of anacardic acid on NF-κB suppression, suggesting the critical role of this enzyme. Overall, our results demonstrate a novel role for anacardic acid in potentially preventing or treating cancer through modulation of NF-κB signaling pathway.
EPO receptor circuits for primary erythroblast survival
Authors: Sathyanarayana Pradeep , Dev Arvind , Fang Jing , Houde Estelle , Bogacheva Olga , Bogachev Oleg , Menon Madhu , Browne Sarah , Pradeep Anamika , Emerson Christine , Wojchowski Don M. 
Published: March 2008

AbstractEPO functions primarily as an erythroblast survival factor, and its antiapoptotic actions have been proposed to involve predominantly PI3-kinase and BCL-X pathways. Presently, the nature of EPO-regulated survival genes has been investigated through transcriptome analyses of highly responsive, primary bone marrow erythroblasts. Two proapoptotic factors, Bim and FoxO3a, were rapidly repressed not only via the wild-type EPOR, but also by PY-deficient knocked-in EPOR alleles. In parallel, Pim1 and Pim3 kinases and Irs2 were induced. For this survival gene set, induction failed via a PY-null EPOR-HM allele, but was restored upon reconstitution of a PY343 STAT5–binding site within a related EPOR-H allele. Notably, EPOR-HM supports erythropoiesis at steady state but not during anemia, while EPOR-H exhibits near wild-type EPOR activities. EPOR-H and the wild-type EPOR (but not EPOR-HM) also markedly stimulated the expression of Trb3 pseudokinase, and intracellular serpin, Serpina-3G. For SERPINA-3G and TRB3, ectopic expression in EPO-dependent progenitors furthermore significantly inhibited apoptosis due to cytokine withdrawal. BCL-XL and BCL2 also were studied, but in highly responsive KitposCD71highTer119neg erythroblasts, neither was EPO modulated. EPOR survival circuits therefore include the repression of Bim plus FoxO3a, and EPOR/PY343/STAT5-dependent stimulation of Pim1, Pim3, Irs2 plus Serpina-3G, and Trb3 as new antiapoptotic effectors.
Epigenetic control of MHC class II expression in tumor-associated macrophages by decoy receptor 3
Authors: Chang Yung-Chi , Chen Tse-Ching , Lee Chun-Ting , Yang Chih-Ya , Wang Hsei-Wei , Wang Chao-Ching , Hsieh Shie-Liang 
Published: March 2008

AbstractDecoy receptor 3 (DcR3) is a member of the TNF receptor superfamily and is up-regulated in tumors originating from a diversity of lineages. DcR3 is capable of promoting angiogenesis, inducing dendritic cell apoptosis, and modulating macrophage differentiation. Since tumor-associated macrophages (TAMs) are the major infiltrating leukocytes in most malignant tumors, we used microarray technology to investigate whether DcR3 contributes to the development of TAMs. Among the DcR3-modulated genes expressed by TAMs, those that encode proteins involved in MHC class II (MHC-II)–dependent antigen presentation were down-regulated substantially, together with the master regulator of MHC-II expression (the class II transactivator, CIITA). The ERK- and JNK-induced deacetylation of histones associated with the CIITA promoters was responsible for DcR3-mediated down-regulation of MHC-II expression. Furthermore, the expression level of DcR3 in cancer cells correlated inversely with HLA-DR levels on TAMs and with the overall survival time of pancreatic cancer patients. The role of DcR3 in the development of TAMs was further confirmed using transgenic mice overexpressing DcR3. This elucidates the molecular mechanism of impaired MHC-II–mediated antigen presentation by TAMs, and raises the possibility that subversion of TAM-induced immunosuppression via inhibition of DcR3 expression might represent a target for the design of new therapeutics.
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
Authors: Lau Christopher , Ng Lydia , Thompson Carol , Pathak Sayan , Kuan Leonard , Jones Allan , Hawrylycz Mike 
Published: March 2008

Abstract

Background
Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL\6J adult mouse brain.

Results
Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.

Conclusion
These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.
Development of a novel data mining tool to find cis-elements in rice gene promoter regions
Authors: Doi Koji , Hosaka Aeni , Nagata Toshifumi , Satoh Kouji , Suzuki Kohji , Mauleon Ramil , Mendoza Michael J , Bruskiewich Richard , Kikuchi Shoshi 
Published: March 2008

Abstract

Background
Information on more than 35 000 full-length Oryza sativa cDNAs, together with associated microarray gene expression data collected under various treatment conditions, has made it feasible to identify motifs that are conserved in gene promoters and may act as cis-regulatory elements with key roles under the various conditions.

Results
We have developed a novel tool that searches for cis-element candidates in the upstream, downstream, or coding regions of differentially regulated genes. The tool first lists cis-element candidates by motif searching based on the supposition that if there are cis-elements playing important roles in the regulation of a given set of genes, they will be statistically overrepresented and will be conserved. Then it evaluates the likelihood scores of the listed candidate motifs by association rule analysis. This strategy depends on the idea that motifs overrepresented in the promoter region could play specific roles in the regulation of expression of these genes. The tool is designed so that any biological researchers can use it easily at the publicly accessible Internet site http://hpc.irri.cgiar.org/tool/nias/ces. We evaluated the accuracy and utility of the tool by using a dataset of auxin-inducible genes that have well-studied cis-elements. The test showed the effectiveness of the tool in identifying significant relationships between cis-element candidates and related sets of genes.

Conclusion
The tool lists possible cis-element motifs corresponding to genes of interest, and it will contribute to the deeper understanding of gene regulatory mechanisms in plants.
Aminopeptidase N (APN)/CD13 inhibitor, Ubenimex, enhances radiation sensitivity in human cervical cancer
Authors: Tsukamoto Hirohisa , Shibata Kiyosumi , Kajiyama Hiroaki , Terauchi Mikio , Nawa Akihiro , Kikkawa Fumitaka 
Published: March 2008

Abstract

Background
Radiotherapy can be used to treat all stages of cervical cancer. For improving local control via radiotherapy, it is important to use additional antitumor agents. Aminopeptidase N (APN)/CD13, a 150-kDa metalloproteinase, is a multifunctional cell surface aminopeptidase with ubiquitous expression. Recent studies have suggested that APN/CD13 plays an important role in tumor progression in several human malignancies.

Methods
We investigated whether the suppression of APN/CD13 using Ubenimex, an inhibitor of APN/CD13 activity, may affect tumor radiosensitivity in cervical cancer cells both in vitro and in vivo. Cell surface APN/CD13 activity in HeLa cells was calculated using alanine-p-nitroanilido as a substrate. For colony formation assays, single-dose radiation and/or Ubenimex were administered to each dish of HeLa cells, and these dishes were cultured for 14 days. Molecular changes of apoptosis were determined by Western blot. Apoptosis was evaluated by Annexin-V PI staining (flow cytometry analysis) and the Tunel method. Moreover, we investigated the effect of combining Ubenimex and low-dose radiation on tumor growth using nude mice.

Results
We demonstrated that Ubenimex enhanced the effectiveness of radiotherapy, acting as a radiosensitizer both in vitro and in vivo. In colony formation assays, a significant decline in clonogenic survival was observed in Ubenimex-treated cells. Mice treated with a combination of radiation and Ubenimex showed a significant prolongation of the tumor-doubling time compared with the control, Ubenimex, or radiation-alone groups. We also showed that ubenimex enhanced radiation-induced apoptosis in vitro and in vivo.

Conclusion
Although further studies are needed, this report suggests that Ubeniemx acts as a radiosensitizer in cervical cancer treatment, and that the inhibition of APN/CD13 activity may represent a new approach for improving the therapeutic efficacy of radiotherapy for uterine cervical cancer.
Transient expression of homologous hairpin RNA interferes with PVY transmission by aphids
Authors: Vargas Marisol , Martínez-García Belén , Díaz-Ruíz José Ramón , Tenllado Francisco 
Published: March 2008

Abstract
Hairpin RNAs have been used to confer resistance to viruses in plants through RNA silencing. However, it has not been demonstrated that RNA silencing was effective against inoculation by aphids of non-persistently transmitted viruses, the major route of plant virus spread in nature. As a proof-of-principle strategy, we made use of Agrobacterium tumefaciens to transiently express a hairpin RNA homologous to Potato virus Y (PVY) in plant tissues. A complete and specific interference with aphid transmission of PVY was achieved by inducers of RNA silencing, as demonstrated by specific siRNAs accumulation in agroinfiltrated tissues. To our knowledge, this is the first report of successful interference with non-persistent transmission of a plant virus using RNA interference.
Immediate gain is long-term loss: Are there foresighted decision makers in the Iowa Gambling Task?
Authors: Chiu Yao-Chu , Lin Ching-Hung , Huang Jong-Tsun , Lin Shuyeu , Lee Po-Lei , Hsieh Jen-Chuen 
Published: March 2008

AbstractBackgroundThe Somatic Marker Hypothesis suggests that normal subjects are "foreseeable" and ventromedial prefrontal patients are "myopic" in making decisions, as the behavior shown in the Iowa Gambling Task. The present study questions previous findings because of the existing confounding between long-term outcome (expected value, EV) and gain-loss frequency variables in the Iowa Gambling Task (IGT). A newly and symmetrically designed gamble, namely the Soochow Gambling Task (SGT), with a high-contrast EV between bad (A, B) and good (C, D) decks, is conducted to clarify the issue about IGT confounding. Based on the prediction of EV (a basic assumption of IGT), participants should prefer to choose good decks C and D rather than bad decks A and B in SGT. In contrast, according to the prediction of gain-loss frequency, subjects should prefer the decks A and B because they possessed relatively the high-frequency gain.MethodsThe present experiment was performed by 48 participants (24 males and 24 females). Most subjects are college students recruited from different schools. Each subject played the computer version SGT first and completed a questionnaire for identifying their final preference. The IGT experimental procedure was mostly followed to assure a similar condition of decision uncertainty.ResultsThe SGT experiment demonstrated that the prediction of gain-loss frequency is confirmed. Most subjects preferred to choose the bad decks A and B than good decks C and D. The learning curve and questionnaire data indicate that subjects can not "hunch" the EV throughout the game. Further analysis of the effect of previous choice demonstrated that immediate gain increases the probability to stay at the same deck.ConclusionSGT provides a balanced structure to clarify the confounding inside IGT and demonstrates that gain-loss frequency rather than EV guides decision makers in these high-ambiguity gambles. Additionally, the choice behavior is mostly following the "gain-stay, lose-randomize" strategy to cope with the uncertain situation. As demonstrated in SGT, immediate gain can bring about a long-term loss under uncertainty. This empirical result may explain some shortsighted behaviors in real life.
VATS intraoperative tattooing to facilitate solitary pulmonary nodule resection
Authors: Willekes Lourens , Boutros Cherif , Goldfarb Michael A. 
Published: March 2008

Abstract

Introduction
Video-assisted thoracic surgery (VATS) has become routine and widely accepted for the removal of solitary pulmonary nodules of unknown etiology. Thoracosopic techniques continue to evolve with better instruments, robotic applications, and increased patient acceptance and awareness.
Several techniques have been described to localize peripheral pulmonary nodules, including pre-operative CT-guided tattooing with methylene blue, CT scan guided spiral/hook wire placement, and transthoracic ultrasound.
As pulmonary surgeons well know, the lung and visceral pleura may appear featureless on top of a pulmonary nodule.

Case description
This paper presents a rapid, direct and inexpensive approach to peripheral lung lesion resection by marking the lung parenchyma on top of the nodule using direct methylene blue injection.

Methods
In two patients with peripherally located lung nodules (n = 3) scheduled for VATS, we used direct methylene blue injection for intraoperative localization of the pulmonary nodule. Our technique was the following: After finger palpation of the lung, a spinal 25 gauge needle was inserted through an existing port and 0.1 ml of methylene blue was used to tattoo the pleura perpendicular to the localized nodule.
The methylene blue tattoo immediately marks the lung surface over the nodule. The surgeon avoids repeated finger palpation, while lining up stapler, graspers and camera, because of the visible tattoo. Our technique eliminates regrasping and repalpating the lung once again to identify a non marked lesion.

Results
Three lung nodules were resected in two patients. Once each lesion was palpated it was marked, and the area was resected with security of accurate localization. All lung nodules were resected in totality with normal lung parenchymal margins. Our technique added about one minute to the operative time. The two patients were discharged home on the second postoperative day, with no morbidity.

Conclusion
VATS with intraoperative tattooing is a safe, easy, and accurate technique to streamline and efficiently resect solitary pulmonary nodules.