bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics of the Lower Stratospheric Circulation Response to ENSO
Authors: Simpson Isla R. , Shepherd Theodore G. , Sigmond Michael 
Published: May 2011

Abstract
A robust feature of the observed response to El Niño–Southern Oscillation (ENSO) is an altered circulation in the lower stratosphere. When sea surface temperatures (SSTs) in the tropical Pacific are warmer there is enhanced upwelling and cooling in the tropical lower stratosphere and downwelling and warming in the midlatitudes, while the opposite is true of cooler SSTs. The midlatitude lower stratospheric response to ENSO is larger in the Southern Hemisphere (SH) than in the Northern Hemisphere (NH).
In this study the dynamical version of the Canadian Middle Atmosphere Model (CMAM) is used to simulate 25 realizations of the atmospheric response to the 1982/83 El Niño and the 1973/74 La Niña. This version of CMAM is a comprehensive high-top general circulation model that does not include interactive chemistry. The observed lower stratospheric response to ENSO is well reproduced by the simulations, allowing them to be used to investigate the mechanisms involved. Both the observed and simulated responses maximize in December–March and so this study focuses on understanding the mechanisms involved in that season.
The response in tropical upwelling is predominantly driven by anomalous transient synoptic-scale wave drag in the SH subtropical lower stratosphere, which is also responsible for the compensating SH midlatitude response. This altered wave drag stems from an altered upward flux of wave activity from the troposphere into the lower stratosphere between 20° and 40°S. The altered flux of wave activity can be divided into two distinct components. In the Pacific, the acceleration of the zonal wind in the subtropics from the warmer tropical SSTs results in a region between the midlatitude and subtropical jets where there is an enhanced source of low phase speed eddies. At other longitudes, an equatorward shift of the midlatitude jet from the extratropical tropospheric response to El Niño results in an enhanced source of waves of higher phase speeds in the subtropics. The altered resolved wave drag is only apparent in the SH and the difference between the two hemispheres can be related to the difference in the climatological jet structures in this season and the projection of the wind anomalies associated with ENSO onto those structures.
Baroclinic Adjustment in an Atmosphere–Ocean Thermally Coupled Model: The Role of the Boundary Layer Processes
Authors: Zhang Yang , Stone Peter H. 
Published: May 2011

Abstract
Baroclinic eddy equilibration and the roles of different boundary layer processes in limiting the baroclinic adjustment are studied using an atmosphere–ocean thermally coupled model. Boundary layer processes not only affect the dynamical constraint of the midlatitude baroclinic eddy equilibration but also are important components in the underlying surface energy budget. The authors' study shows that baroclinic eddies, with the strong mixing of the surface air temperature, compete against the fast boundary layer thermal damping and enhance the meridional variation of surface sensible heat flux, acting to reduce the meridional gradient of the surface temperature. Nevertheless, the requirement of the surface energy balance indicates that strong surface baroclinicity is always maintained in response to the meridionally varying solar radiation. With the strong surface baroclinicity and the boundary layer processes, the homogenized potential vorticity (PV) suggested in the baroclinic adjustment are never observed near the surface or in the boundary layer.
Although different boundary layer processes affect baroclinic eddy equilibration differently with more dynamical feedbacks and time scales included in the coupled system, their influence in limiting the PV homogenization is more uniform compared with the previous uncoupled runs. The boundary layer PV structure is more determined by the strength of the boundary layer damping than the surface baroclinicity. Stronger boundary layer processes always prevent the lower-level PV homogenization more efficiently. Above the boundary layer, a relatively robust PV structure with homogenized PV around 600–800 hPa is obtained in all of the simulations. The detailed mechanisms through which different boundary layer processes affect the equilibration of the coupled system are discussed in this study.
Improved Normalization of the Size Distribution of Atmospheric Particles Retrieved from Aureole Measurements Using the Diffraction Approximation
Authors: DeVore J. G. 
Published: May 2011

Abstract
This paper describes an improvement in the diffraction approximation used to retrieve the size distribution of atmospheric particles from solar aureole radiance measurements. Normalization using total optical thickness based on measurement of the solar disk radiance is replaced with one based on the aureole profile radiance itself. Retrievals involving model calculations for power-law distributions of water droplets show significant improvement using the new algorithm. Tests involving two empirical particle size distributions, one for cirrus and another for aerosols, also show improvement using the new normalization algorithm. Comparisons of the diffraction approximation algorithms with a numerical inversion algorithm found that the accuracy of the latter was higher for two different bimodal aerosol distributions. The role envisioned for the diffraction approximation is in estimating the size distribution of large particles in clouds and especially cirrus.
Recognition by family members that relatives with neurodegenerative disease are likely to die within a year: A meta-ethnography
Authors: Hubbard G , McLachlan K , Forbat L , Munday D 
Published: May 2011

Objective: To synthesize evidence of family members recognizing that their relative is likely to die within the year, and identifying the need for palliative care. Design: A meta-ethnography of studies of family members in multiple sclerosis (MS), Parkinson’s disease (PD) and motor neuron disease (MND). Review methods: Systematic search in electronic databases; thematic synthesis guided by the principles of meta-ethnography, which is a method for thematic synthesis of qualitative studies. Results: Nine articles were included. The results of the synthesis identified two key themes. First, family members are intimately aware of changes in their relative’s health and well-being. Sub-themes include family member awareness of different and progressive stages of the disease, noticing deterioration, noticing decline in functional abilities and recognizing that their relative will die. The second key theme is dilemmas of being involved in prognostication. Sub-themes include family member ambivalence toward hearing about prognostication, health professionals not being knowledgeable of the disease and family reluctance to receive palliative care. Conclusions: Family members monitor and recognize changes in their relative with PD, MND and MS and in themselves. Thus, drawing on the expertise of family members may be a useful tool for prognostication.
Cortical inhibition at rest and under a focused attention challenge in adults with migraine with and without aura
Authors: Maier Joachim , Sebastian Imke , Weisbrod Matthias , Freitag Christine M , Resch Franz , Bender Stephan 
Published: May 2011

Objectives: We aimed to further elucidate the functional and attentional regulation of cortical excitability in migraine patients. Methods: We investigated the cortical silent period (CSP) after transcranial magnetic stimulation as a measure of cortical inhibition under three conditions: resting condition, cortical preactivation during reaction preparation, and during the post-processing of a motor response using a visual contingent negative variation paradigm in adults with migraine with aura, migraine without aura and healthy controls. Results: CSP was reduced in individuals with migraine with aura and unaffected in those with migraine without aura under resting conditions. Along with the intensity of transcranial magnetic stimulation, CSP increased equally in all groups (equal slopes). Furthermore, the functional challenge by a contingent negative variation task requiring focused sustained attention led to a comparable reduction of CSP duration in all groups. Discussion: Our data provide further hints towards the conclusion that a specific cortical inhibition deficit in migraine with aura but not migraine without aura is due to a tonic imbalance and not related to increased reactions to phasic stressors. Given that CSP at rest is related to GABA-ergic inhibition whereas the CSP reduction during late contingent negative variation is thought to be related to dopaminergic disinhibition in the basal ganglia, our results point towards reduced GABA-ergic cortical inhibition related to dysfunctional thalamo-cortical loops, especially in migraine with aura.
The Effect of Music Therapy on Hospitalized Psychiatric Patients’ Anxiety, Finger Temperature, and Electroencephalography
Authors: Yang Chyn-Yng , Chen Chiung-Hua , Chu Hsin , Chen Wen-Chun , Lee Tso-Ying , Chen Shyi-Gen , Chou Kuei-Ru 
Published: May 2011

Purpose: This study aimed to explore the effectiveness of music therapy in reducing anxiety in hospitalized psychiatric patients. Methodology: The authors used a randomized clinical trial design and randomly allocated the 24 enrolled participants to the experimental or the control group. Patients in the experimental group received music therapy in a therapy room at a set time for 30 min each morning for 11 days. The authors administered the Beck Anxiety Inventory (BAI) and measured skin temperature and brain waves to determine anxiety level before, during, and after music therapy. Results: Experimental group participants had lower scores on the BAI than control participants, after the music therapy ( z = −2.0, p < .05) and at 1-week follow-up ( z = −2.2, p < .05), indicating that they were experiencing significantly less anxiety. The mean BAI anxiety score fell in the experimental group from 23.9 ( SD = 9.9) at baseline to 13.9 ( SD = 8.8), after music therapy, and 12.7. ( SD = 10.5) at follow-up. The experimental group demonstrated a significant elevation in the average alpha electroencephalographic (EEG) percentage (from 38.1% to 46.7%) and a reduction in the average beta EEG percentage (from 61.9% to 53.4%) after the music therapy. After adjusting for change in patient finger temperature on the first day, mean change in finger temperature did not differ significantly between the experimental and control groups. Conclusions: Music therapy can relieve anxiety in hospitalized psychiatric patients and help them achieve a state of relaxation.
Trends in annualized relapse rates in relapsing–remitting multiple sclerosis and consequences for clinical trial design
Authors: Nicholas Richard , Straube Sebastian , Schmidli Heinz , Schneider Simon , Friede Tim 
Published: May 2011

Background: Sample size calculation is a key aspect in the planning of any trial. Planning a randomized placebo-controlled trial in relapsing–remitting multiple sclerosis (RRMS) requires knowledge of the annualized relapse rate (ARR) in the placebo group. Objectives: This paper aims (i) to characterize the uncertainty in ARR by conducting a systematic review of placebo-controlled, randomized trials in RRMS and by modelling the ARR over time; and (ii) to assess the feasibility and utility of blinded sample size re-estimation (BSSR) procedures in RRMS. Methods: A systematic literature review was carried out by searching PubMed, Ovid Medline and the Cochrane Register of Controlled Trials. The placebo ARRs were modelled by negative binomial regression. Computer simulations were conducted to assess the utility of BSSR in RRMS. Results: Data from 26 placebo-controlled randomized trials were included in this analysis. The placebo ARR decreased by 6.2% per year ( p < 0.0001; 95% CI (4.2%; 8.1%)) resulting in substantial uncertainty in the planning of future trials. BSSR was shown to be feasible and to maintain power at a prespecified level also if the ARR was misspecified in the planning phase. Conclusions: Our investigations confirmed previously reported trends in ARR. In this context adaptive strategies such as BSSR designs are recommended for consideration in the planning of future trials in RRMS.
Examining the benefits of combining two learning strategies on recall of functional information in persons with multiple sclerosis
Authors: Goverover Yael , Basso Michael , Wood Hali , Chiaravalloti Nancy , DeLuca John 
Published: May 2011

Background: Forgetfulness occurs commonly in people with multiple sclerosis (MS), but few treatments alleviate this problem. Objective: This study examined the combined effect of two cognitive rehabilitation strategies to improve learning and memory in MS: self-generation and spaced learning. The hypothesis was that the combination of spaced learning and self-generation would yield better learning and memory recall performance than spaced learning alone. Method: Using a within groups design, 20 participants with MS and 18 healthy controls (HC) were presented with three tasks (learning names, appointment, and object location), each in three learning conditions (Massed, Spaced Learning, and combination of spaced and generated information). Participants were required to recall the information they learned in each of these conditions immediately and 30 min following the initial presentation. Results: The combination of spaced learning and self-generation yielded better recall than did spaced learning alone. In turn, spaced learning resulted in better recall than the massed rehearsal condition. Conclusions: These findings reveal that the combination of these two learning strategies may possess utility as a cognitive rehabilitation strategy.
Cooperative function of CCR7 and lymphotoxin in the formation of a lymphoma-permissive niche within murine secondary lymphoid organs
Authors: Rehm Armin , Mensen Angela , Schradi Kristina , Gerlach Kerstin , Wittstock Stefanie , Winter Susann , Büchner Gilbert , Dörken Bernd , Lipp Martin , Höpken Uta E. 
Published: May 2011

Abstract
Lymphoma cell survival and progression are putatively dependent on a specific microanatomic localization within secondary lymphoid organs. Despite compelling data correlating homeostatic chemokine receptor expression and human lymphoma pathogenesis, genetic models that either mimic lymphoma dissemination or dissect a crosstalk of lymphoma and stromal cells are missing. Applying the genetically tractable Eμ-Myc transgenic mouse model, we show that the chemokine receptor CCR7 regulates Eμ-Myc lymphoma homing to lymph nodes and distinctive microanatomic sites of the spleen. CCR7-controlled access of lymphoma cells to the splenic T-cell zone led to a significant survival advantage compared with CCR7-deficient lymphoma cells, which were excluded from this zone. Within the niche, lymphoma cells stimulated a reciprocal cross-talk with gp38+ fibroblastic reticular cells. This reciprocal cooperation program was mediated by lymphoma B cell–presented lymphotoxin, which acted on lymphotoxin-β–receptor-bearing stromal cells followed by alteration of stromal cellular composition. Cross-talk inhibition by lymphotoxin-α deletion and using a lymphotoxin-β receptor-immunoglobulin fusion protein impaired lymphoma growth. Thus, abrogation of CCR7-governed migration and of sustained lymphotoxin signaling could provide new targets in lymphoma therapy.
Endogenous oncogenic Nras mutation initiates hematopoietic malignancies in a dose- and cell type-dependent manner
Authors: Wang Jinyong , Liu Yangang , Li Zeyang , Wang Zhongde , Tan Li Xuan , Ryu Myung-Jeom , Meline Benjamin , Du Juan , Young Ken H. , Ranheim Erik , Chang Qiang , Zhang Jing 
Published: May 2011

Abstract
Both monoallelic and biallelic oncogenic NRAS mutations are identified in human leukemias, suggesting a dose-dependent role of oncogenic NRAS in leukemogenesis. Here, we use a hypomorphic oncogenic Nras allele and a normal oncogenic Nras allele (Nras G12Dhypo and Nras G12D, respectively) to create a gene dose gradient ranging from 25% to 200% of endogenous Nras G12D/+. Mice expressing Nras G12Dhypo/G12Dhypo develop normally and are tumor-free, whereas early embryonic expression of Nras G12D/+ is lethal. Somatic expression of Nras G12D/G12D but not Nras G12D/+ leads to hyperactivation of ERK, excessive proliferation of myeloid progenitors, and consequently an acute myeloproliferative disease. Using a bone marrow transplant model, we previously showed that ∼ 95% of animals receiving Nras G12D/+ bone marrow cells develop chronic myelomonocytic leukemia (CMML), while ∼ 8% of recipients develop acute T-cell lymphoblastic leukemia/lymphoma [TALL] (TALL-het). Here we demonstrate that 100% of recipients transplanted with Nras G12D/G12D bone marrow cells develop TALL (TALL-homo). Although both TALL-het and -homo tumors acquire Notch1 mutations and are sensitive to a γ-secretase inhibitor, endogenous Nras G12D/+ signaling promotes TALL through distinct genetic mechanism(s) from Nras G12D/G12D. Our data indicate that the tumor transformation potential of endogenous oncogenic Nras is both dose- and cell type-dependent.
The identification and characterization of zebrafish hematopoietic stem cells
Authors: Ma Dongdong , Zhang Jing , Lin Hui-feng , Italiano Joseph , Handin Robert I. 
Published: May 2011

AbstractHSCs are defined by their ability to self-renew and maintain hematopoiesis throughout the lifespan of an organism. The optical clarity of their embryos and the ease of genetic manipulation make the zebrafish (Danio rerio) an excellent model for studying hematopoiesis. Using flow cytometry, we identified 2 populations of CD41-GFP+ cells (GFPhi and GFPlo) in the whole kidney marrow of Tg(CD41:GFP) zebrafish. Past studies in humans and mice have shown that CD41 is transiently expressed in the earliest hematopoietic progenitors and is then silenced, reappearing in the platelet/thrombocyte lineage. We have transplanted flow-sorted GFPhi and GFPlo cells into irradiated adult zebrafish and assessed long-term hematopoietic engraftment. Transplantation of GFPhi cells did not reconstitute hematopoiesis. In contrast, we observed multilineage hematopoiesis up to 68 weeks after primary and secondary transplantation of GFPlo cells. We detected the CD41-GFP transgene in all major hematopoietic lineages and CD41-GFP+ cells in histologic sections of kidneys from transplant recipients. These studies show that CD41-GFPlo cells fulfill generally accepted criteria for HSCs. The identification of fluorescent zebrafish HSCs, coupled with our ability to transplant them into irradiated adult recipients, provide a valuable new tool to track HSC homing, proliferation, and differentiation into hematopoietic cells.
Neuropilin-1 promotes VEGFR-2 trafficking through Rab11 vesicles thereby specifying signal output
Authors: Ballmer-Hofer Kurt , Andersson Anneli E. , Ratcliffe Laura E. , Berger Philipp 
Published: May 2011

AbstractVascular endothelial growth factors (VEGFs) regulate blood and lymph vessel development by activating 3 receptor tyrosine kinases (RTKs), VEGFR-1, -2, and -3, and by binding to coreceptors such as neuropilin-1 (NRP-1). We investigated how different VEGF-A isoforms, in particular VEGF-A165a and VEGF-A165b, control the balance between VEGFR-2 recycling, degradation, and signaling. Stimulation of cells with the NRP-1–binding VEGF-A165a led to sequential NRP-1–mediated VEGFR-2 recycling through Rab5, Rab4, and Rab11 vesicles. Recycling was accompanied by dephosphorylation of VEGFR-2 between Rab4 and Rab11 vesicles and quantitatively and qualitatively altered signal output. In cells stimulated with VEGF-A165b, an isoform unable to bind NRP-1, VEGFR-2 bypassed Rab11 vesicles and was routed to the degradative pathway specified by Rab7 vesicles. Deletion of the GIPC (synectin) binding motif of NRP-1 prevented transition of VEGFR-2 through Rab11 vesicles and attenuated signaling. Coreceptor engagement was specific for VEGFR-2 because EGFR recycled through Rab11 vesicles in the absence of known coreceptors. Our data establish a distinct role of NRP-1 in VEGFR-2 signaling and reveal a general mechanism for the function of coreceptors in modulating RTK signal output.
Paraproteins of familial MGUS/multiple myeloma target family-typical antigens: hyperphosphorylation of autoantigens is a consistent finding in familial and sporadic MGUS/MM
Authors: Grass Sandra , Preuss Klaus-Dieter , Thome Stephan , Weisenburger Dennis D. , Witt Vinetta , Lynch Jane , Zettl Florian , Trümper Lorenz , Fadle Natalie , Regitz Evi , Lynch Henry , Pfreundschuh Michael 
Published: May 2011

Abstract
Paratarg-7 (P-7) is a frequent paraprotein target in monoclonal gammopathy of undetermined significance (MGUS), multiple myeloma (MM), and Waldenström macroglobulinemia. Patients with P-7-specific paraproteins carry a hyperphosphorylated paratarg-7 (pP-7). Because pP-7 carrier state is dominantly inherited, we determined the paraprotein targets in 4 families with familial MGUS/MM. No antigenic target was identified for the paraproteins from 2 members of one family. Paraproteins from affected members of 2 other families targeted P-7, and paraproteins from 4 affected members of a fourth family targeted P-8, which is encoded by the ATG13 gene. P-8 was hyperphosphorylated in the affected family members (pP-8) and pP-8 carrier state is inherited in a dominant fashion. Six additional autoantigenic nonfamilial paraprotein targets were also hyperphosphorylated in the respective patients compared with normal controls. We conclude that paraproteins of affected members with familial MGUS/MM share family-typical hyperphosphorylated antigens and hyperphosphorylation of paraprotein targets might be a general mechanism underlying the pathogenesis of MGUS/MM.
PRIN: a predicted rice interactome network
Authors: Gu Haibin , Zhu Pengcheng , Jiao Yinming , Meng Yijun , Chen Ming 
Published: May 2011

Abstract

Background
Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed by mass spectrometry are widely used in model organisms, the progress of protein-protein interactions detection in plants is rather slow. With this motivation, our work presents a computational approach to predict protein-protein interactions in Oryza sativa.

Results
To better understand the interactions of proteins in Oryza sativa, we have developed PRIN, a Predicted Rice Interactome Network. Protein-protein interaction data of PRIN are based on the interologs of six model organisms where large-scale protein-protein interaction experiments have been applied: yeast (Saccharomyces cerevisiae), worm (Caenorhabditis elegans), fruit fly (Drosophila melanogaster), human (Homo sapiens), Escherichia coli K12 and Arabidopsis thaliana. With certain quality controls, altogether we obtained 76,585 non-redundant rice protein interaction pairs among 5,049 rice proteins. Further analysis showed that the topology properties of predicted rice protein interaction network are more similar to yeast than to the other 5 organisms. This may not be surprising as the interologs based on yeast contribute nearly 74% of total interactions. In addition, GO annotation, subcellular localization information and gene expression data are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization.

Conclusions
PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended the current available protein-protein interaction data of rice with a computational approach, which will certainly provide further insights into rice functional genomics and systems biology.
PRIN is available online at http://bis.zju.edu.cn/prin/.