bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oceanic Internal-Wave Field: Theory of Scale-Invariant Spectra
Authors: Lvov Yuri V. , Polzin Kurt L. , Tabak Esteban G. , Yokoyama Naoto 
Published: January 2011

Abstract
Steady scale-invariant solutions of a kinetic equation describing the statistics of oceanic internal gravity waves based on wave turbulence theory are investigated. It is shown in the nonrotating scale-invariant limit that the collision integral in the kinetic equation diverges for almost all spectral power-law exponents. These divergences come from resonant interactions with the smallest horizontal wavenumbers and/or the largest horizontal wavenumbers with extreme scale separations.
A small domain is identified in which the scale-invariant collision integral converges and numerically find a convergent power-law solution. This numerical solution is close to the Garrett–Munk spectrum. Power-law exponents that potentially permit a balance between the infrared and ultraviolet divergences are investigated. The balanced exponents are generalizations of an exact solution of the scale-invariant kinetic equation, the Pelinovsky–Raevsky spectrum. A small but finite Coriolis parameter representing the effects of rotation is introduced into the kinetic equation to determine solutions over the divergent part of the domain using rigorous asymptotic arguments. This gives rise to the induced diffusion regime.
The derivation of the kinetic equation is based on an assumption of weak nonlinearity. Dominance of the nonlocal interactions puts the self-consistency of the kinetic equation at risk. However, these weakly nonlinear stationary states are consistent with much of the observational evidence.
Tropical–Extratropical Teleconnections in Boreal Summer: Observed Interannual Variability*
Authors: Ding Qinghua , Wang Bin , Wallace John M. , Branstator Grant 
Published: January 2011

Abstract
Maximum covariance analysis is performed on the fields of boreal summer, tropical rainfall, and Northern Hemisphere (NH) 200-hPa height for the 62-yr period of record of 1948–2009. The leading mode, which appears preferentially in summers preceding the peak phases of the El Niño–Southern Oscillation (ENSO) cycle, involves a circumglobal teleconnection (CGT) pattern in the NH extratropical 200-hPa height field observed in association with Indian monsoon rainfall anomalies. The second mode, which tends to occur in summers following ENSO peak phases, involves a western Pacific–North America (WPNA) teleconnection pattern in the height field observed in association with western North Pacific summer monsoon rainfall anomalies. The CGT pattern is primarily a zonally oriented wave train along the westerly waveguide, while the WPNA pattern is a wave train emanating from the western Pacific monsoon trough and following a great circle. The CGT is accompanied by a pronounced tropical–extratropical seesaw in the zonally symmetric geopotential height and temperature fields, and the WPNA is observed in association with hemispherically uniform anomalies. These ENSO-related features modulate surface air temperature in both the tropics and extratropics. ENSO also affects the wave structure of the CGT and WPNA indirectly, by modulating the strengths of the Indian and western North Pacific monsoons. Linear barotropic mechanisms, including energy propagation and barotropic instability of the basic-state flow, also act to shape and maintain the CGT. The implications of these findings for seasonal prediction of the NH extratropical circulation are discussed.
The Relationship between Land–Ocean Surface Temperature Contrast and Radiative Forcing
Authors: Lambert F. Hugo , Webb Mark J. , Joshi Manoj M. 
Published: January 2011

Abstract
Previous work has demonstrated that observed and modeled climates show a near-time-invariant ratio of mean land to mean ocean surface temperature change under transient and equilibrium global warming. This study confirms this in a range of atmospheric models coupled to perturbed sea surface temperatures (SSTs), slab (thermodynamics only) oceans, and a fully coupled ocean. Away from equilibrium, it is found that the atmospheric processes that maintain the ratio cause a land-to-ocean heat transport anomaly that can be approximated using a two-box energy balance model. When climate is forced by increasing atmospheric CO2 concentration, the heat transport anomaly moves heat from land to ocean, constraining the land to warm in step with the ocean surface, despite the small heat capacity of the land. The heat transport anomaly is strongly related to the top-of-atmosphere radiative flux imbalance, and hence it tends to a small value as equilibrium is approached. In contrast, when climate is forced by prescribing changes in SSTs, the heat transport anomaly replaces “missing” radiative forcing over land by moving heat from ocean to land, warming the land surface. The heat transport anomaly remains substantial in steady state. These results are consistent with earlier studies that found that both land and ocean surface temperature changes may be approximated as local responses to global mean radiative forcing. The modeled heat transport anomaly has large impacts on surface heat fluxes but small impacts on precipitation, circulation, and cloud radiative forcing compared with the impacts of surface temperature change. No substantial nonlinearities are found in these atmospheric variables when the effects of forcing and surface temperature change are added.
Effectiveness of community-based ambulation training for walking function of post-stroke hemiparesis: a randomized controlled pilot trial
Authors: Park Hyun-Ju , Oh Duck-Won , Kim Suhn-Yeop , Choi Jong-Duk 
Published: January 2011

Objective: To investigate the effect of community-based ambulation training on walking function of patients with post-stroke hemiparesis. Design: Randomized, single-blind, controlled pilot study. Setting: Inpatient rehabilitation hospital. Subjects: Twenty-five subjects were randomly assigned to either the experimental group or the control group, with 13 and 12 subjects, respectively. Interventions: All subjects received a routine physical therapy. The subjects in the experimental group also received community-based ambulation training, which was performed for an hour, once a day, three times a week for a four-week period. Main measures: Ten-metre walk test, 6-minute walk test, community walk test, walking ability questionnaire and activities-specific balance confidence scale before and after the intervention. Results: The change values of the 10-m walk test (0.21 ± 0.12 m/s versus 0.07 ± 0.10 m/s), community walk test (−13.61 ± 10.31 minutes versus −3.27 ± 11.99 minutes), walking ability questionnaire (6.15 ± 3.60 score versus 2.75 ± 2.38 score) and activities-specific balance confidence scale (17.45 ± 11.55 score versus 2.55 ± 10.14 score) were significantly higher in the experimental group than in the control group ( P < 0.05). At post-test, the 10-m walk test was significantly higher in the experimental group than in the control group (0.72 ± 0.24 m/s versus 0.50 ± 0.23 m/s) ( P < 0.05). In the experimental group, there were significant differences for all variables between pre-test and post-test ( P < 0.01), whereas the subjects of the control group showed a significant difference in only the walking ability questionnaire ( P < 0.01). Conclusions: The findings demonstrate that community-based ambulation training can be helpful in improving walking ability of patients with post-stroke hemiparesis and may be used as a practical adjunct to routine rehabilitation therapy.
Differential requirements for CD45 in NK-cell function reveal distinct roles for Syk-family kinases
Authors: Hesslein David G. T. , Palacios Emil H. , Sun Joseph C. , Beilke Joshua N. , Watson Susan R. , Weiss Arthur , Lanier Lewis L. 
Published: January 2011

AbstractThe protein tyrosine phosphatase CD45 is an important regulator of Src-family kinase activity. We found that in the absence of CD45, natural killer (NK) cells are defective in protecting the host from mouse cytomegalovirus infection. We show that although CD45 is necessary for all immunoreceptor tyrosine–based activation motif (ITAM)–specific NK-cell functions and processes such as degranulation, cytokine production, and expansion during viral infection, the impact of CD45 deficiency on ITAM signaling differs depending on the downstream function. CD45-deficient NK cells are normal in their response to inflammatory cytokines when administered ex vivo and in the context of viral infection. Syk and ζ chain–associated protein kinase 70 (Zap70) are thought to play redundant roles in transmitting ITAM signals in NK cells. We show that Syk, but not Zap70, controls the remaining CD45-independent, ITAM-specific NK-cell functions, demonstrating a functional difference between these 2 Syk-kinase family members in primary NK cells.
Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes
Authors: Piccaluga Pier Paolo , De Falco Giulia , Kustagi Manjunath , Gazzola Anna , Agostinelli Claudio , Tripodo Claudio , Leucci Eleonora , Onnis Anna , Astolfi Annalisa , Sapienza Maria Rosaria , Bellan Cristiana , Lazzi Stefano , Tumwine Lynnette , Mawanda Michael , Ogwang Martin , Calbi Valeria , Formica Serena , Califano Andrea , Pileri Stefano A. , Leoncini Lorenzo 
Published: January 2011

AbstractBurkitt lymphoma (BL) is classified into 3 clinical subsets: endemic, sporadic, and immunodeficiency-associated BL. So far, possible differences in their gene expression profiles (GEPs) have not been investigated. We studied GEPs of BL subtypes, other B-cell lymphomas, and B lymphocytes; first, we found that BL is a unique molecular entity, distinct from other B-cell malignancies. Indeed, by unsupervised analysis all BLs clearly clustered apart of other lymphomas. Second, we found that BL subtypes presented slight differences in GEPs. Particularly, they differed for genes involved in cell cycle control, B-cell receptor signaling, and tumor necrosis factor/nuclear factor κB pathways. Notably, by reverse engineering, we found that endemic and sporadic BLs diverged for genes dependent on RBL2 activity. Furthermore, we found that all BLs were intimately related to germinal center cells, differing from them for molecules involved in cell proliferation, immune response, and signal transduction. Finally, to validate GEP, we applied immunohistochemistry to a large panel of cases and showed that RBL2 can cooperate with MYC in inducing a neoplastic phenotype in vitro and in vivo. In conclusion, our study provided substantial insights on the pathobiology of BLs, by offering novel evidences that may be relevant for its classification and possibly future treatment.
High interferon type I responses in the lung, plasma and spleen during highly pathogenic H5N1 infection of chicken
Authors: Moulin Hervé R , Liniger Matthias , Python Sylvie , Guzylack-Piriou Laurence , Ocaña-Macchi Manuela , Ruggli Nicolas , Summerfield Artur 
Published: January 2011

Abstract
This study shows that high pathogenic H5N1 influenza virus infection of chicken induced high levels of bioactive interferon type I in the lung (4.3 × 105 U/mg tissue), plasma (1.1 × 105 U/mL), and spleen (9.1 × 105 U/mg tissue). In contrast, a low pathogenic attenuated H5N1 vaccine strain only induced approximately 24 times less IFN in the lung, 441 times less in the spleen and 649 less in the plasma. This was in the same range as a reassortant carrying the HA from the vaccine strain and the remaining genes from the high pathogenic virus. On the other hand, a reassortant virus with the HA from the high pathogenic H5N1 with the remaining genes from the vaccine strain had intermediate levels of IFN. The level of interferon responses related to the viral load, and those in the spleen and blood to the spread of virus to lymphoid tissue, as well as disease severity. In vitro, the viruses did not induce interferon in chicken embryonic fibroblasts, but high levels in splenocytes, with not clear relationship to pathogenicity and virulence. This, and the responses also with inactivated viruses imply the presence of plasmacytoid dendritic cell-like leukocytes within the chicken immune system, possibly responsible for the high interferon responses during H5N1 infection. Our data also indicate that the viral load as well as the cleavability of the HA enabling systemic spread of the virus are two major factors controlling systemic IFN responses in chicken.
Enhanced glutamate, IP3 and cAMP activity in the cerebral cortex of Unilateral 6-hydroxydopamine induced Parkinson's rats: Effect of 5-HT, GABA and bone marrow cell supplementation
Authors: Nandhu MS , Paul Jes , Kuruvilla Korah P , Malat Anitha , Romeo Chinthu , Paulose CS 
Published: January 2011

Abstract
Parkinson's disease is characterized by progressive cell death in the substantia nigra pars compacta, which leads to dopamine depletion in the striatum and indirectly to cortical dysfunction. Increased glutamatergic transmission in the basal ganglia is implicated in the pathophysiology of Parkinson's disease and glutamate receptor mediated excitotoxicity has been suggested to be one of the possible causes of the neuronal degeneration. In the present study, the effects of serotonin, gamma-aminobutyric acid and bone marrow cells infused intranigrally to substantia nigra individually and in combination on unilateral 6-hydroxydopamine induced Parkinson's rat model was analyzed. Scatchard analysis of total glutamate and NMDA receptor binding parameters showed a significant increase in Bmax (P < 0.001) in the cerebral cortex of 6-hydroxydopamine infused rat compared to control. Real Time PCR amplification of NMDA2B, mGluR5, bax, and ubiquitin carboxy-terminal hydrolase were up regulated in cerebral cortex of 6-hydroxydopamine infused rats compared to control. Gene expression studies of GLAST, ά-Synuclien and Cyclic AMP response element-binding protein showed a significant (P < 0.001) down regulation in 6-OHDA infused rats compared to control. Behavioural studies were carried out to confirm the biochemical and molecular studies. Serotonin and GABA along with bone marrow cells in combination showed reversal of glutamate receptors and behaviour abnormality shown in the Parkinson's rat model. The therapeutic significance in Parkinson's disease is of prominence.
Hedgehog overexpression leads to the formation of prostate cancer stem cells with metastatic property irrespective of androgen receptor expression in the mouse model
Authors: Chang Han-Hsin , Chen Bo-Yie , Wu Chia-Yung , Tsao Zih-Jay , Chen Ying-Yu , Chang Chin-Pao , Yang Chi-Rei , Lin David Pei-Cheng 
Published: January 2011

Abstract

Background
Hedgehog signalling has been implicated in prostate tumorigenesis in human subjects and mouse models, but its effects on transforming normal basal/stem cells toward malignant cancer stem cells remain poorly understood.

Methods
We produced pCX-shh-IG mice that overexpress Hedgehog protein persistently in adult prostates, allowing for elucidation of the mechanism during prostate cancer initiation and progression. Various markers were used to characterize and confirm the transformation of normal prostate basal/stem cells into malignant cancer stem cells under the influence of Hedgehog overexpression.

Results
The pCX-shh-IG mice developed prostatic intraepithelial neoplasia (PIN) that led to invasive and metastatic prostate cancers within 90 days. The prostate cancer was initiated through activation of P63+ basal/stem cells along with simultaneous activation of Hedgehog signalling members, suggesting that P63+/Patch1+ and P63+/Smo+ cells may serve as cancer-initiating cells and progress into malignant prostate cancer stem cells (PCSCs). In the hyperplastic lesions and tumors, the progeny of PCSCs differentiated into cells of basal-intermediate and intermediate-luminal characteristics, whereas rare ChgA+ neuroendocrine differentiation was seen. Furthermore, in the metastatic loci within lymph nodes, kidneys, and lungs, the P63+ PCSCs formed prostate-like glandular structures, characteristic of the primitive structures during early prostate development. Besides, androgen receptor (AR) expression was detected heterogeneously during tumor progression. The existence of P63+/AR-, CK14+/AR- and CD44+/AR- progeny indicates direct procurement of AR- malignant cancer trait.

Conclusions
These data support a cancer stem cell scenario in which Hedgehog signalling plays important roles in transforming normal prostate basal/stem cells into PCSCs and in the progression of PCSCs into metastatic tumor cells.
Pathway-based analysis using reduced gene subsets in genome-wide association studies
Authors: Zhao Jingyuan , Gupta Simone , Seielstad Mark , Liu Jianjun , Thalamuthu Anbupalam 
Published: January 2011

AbstractBackgroundSingle Nucleotide Polymorphism (SNP) analysis only captures a small proportion of associated genetic variants in Genome-Wide Association Studies (GWAS) partly due to small marginal effects. Pathway level analysis incorporating prior biological information offers another way to analyze GWAS's of complex diseases, and promises to reveal the mechanisms leading to complex diseases. Biologically defined pathways are typically comprised of numerous genes. If only a subset of genes in the pathways is associated with disease then a joint analysis including all individual genes would result in a loss of power. To address this issue, we propose a pathway-based method that allows us to test for joint effects by using a pre-selected gene subset. In the proposed approach, each gene is considered as the basic unit, which reduces the number of genetic variants considered and hence reduces the degrees of freedom in the joint analysis. The proposed approach also can be used to investigate the joint effect of several genes in a candidate gene study.ResultsWe applied this new method to a published GWAS of psoriasis and identified 6 biologically plausible pathways, after adjustment for multiple testing. The pathways identified in our analysis overlap with those reported in previous studies. Further, using simulations across a range of gene numbers and effect sizes, we demonstrate that the proposed approach enjoys higher power than several other approaches to detect associated pathways.ConclusionsThe proposed method could increase the power to discover susceptibility pathways and to identify associated genes using GWAS. In our analysis of genome-wide psoriasis data, we have identified a number of relevant pathways for psoriasis.
easyDAS: Automatic creation of DAS servers
Authors: Moreno Bernat Gel , Jenkinson Andrew M , Jimenez Rafael C , Peypoch Xavier Messeguer , Hermjakob Henning 
Published: January 2011

Abstract

Background
The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process.

Results
Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license.

Conclusions
easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community.
Epithelial cell-directed efferocytosis in the post-partum mammary gland is necessary for tissue homeostasis and future lactation
Authors: Sandahl Melissa , Hunter Debra M , Strunk Karen E , Earp H Shelton , Cook Rebecca S 
Published: January 2011

Abstract

Background
Mammary glands harbor a profound burden of apoptotic cells (ACs) during post-lactational involution, but little is known regarding mechanisms by which ACs are cleared from the mammary gland, or consequences if this process is interrupted. We investigated AC clearance, also termed efferocytosis, during post-lactational remodeling, using mice deficient for MerTK, Axl, and Tyro3, three related receptor tyrosine kinases (RTKs) regulating macrophage-mediated efferocytosis in monocytes. MerTK expression, apoptosis and the accumulation of apoptotic debris were examined in histological sections of MerTK-deficient, Axl/Tyro3-deficient, and wild-type mammary glands harvested at specific time points during lactation and synchronized involution. The ability of primary mammary epithelial cells (MECs) to engulf ACs was assessed in culture. Transplant of MerTK-deficient mammary epithelium into cleared WT mammary fat pads was used to assess the contribution of WT mammary macrophages to post-lactational efferocytosis.

Results
ACs induced MerTK expression in MECs, resulting in elevated MerTK levels at the earliest stages of involution. Loss of MerTK resulted in AC accumulation in post-lactational MerTK-deficient mammary glands, but not in Axl and Tyro3-deficient mammary glands. Increased vascularization, fibrosis, and epithelial hyperproliferation were observed in MerTK-deficient mammary glands through at least 60 days post-weaning, due to failed efferocytosis after lactation, but did not manifest in nulliparous mice. WT host-derived macrophages failed to rescue efferocytosis in transplanted MerTK-deficient mammary epithelium.

Conclusion
Efferocytosis by MECs through MerTK is crucial for mammary gland homeostasis and function during the post-lactational period. Efferocytosis by MECs thus limits pathologic consequences associated with the apoptotic load following lactation.
Normal social seeking behavior, hypoactivity and reduced exploratory range in a mouse model of Angelman syndrome
Authors: Allensworth Melody , Saha Anand , Reiter Lawrence T , Heck Detlef H 
Published: January 2011

Abstract

Background
Angelman syndrome (AS) is a neurogenetic disorder characterized by severe developmental delay with mental retardation, a generally happy disposition, ataxia and characteristic behaviors such as inappropriate laughter, social-seeking behavior and hyperactivity. The majority of AS cases are due to loss of the maternal copy of the UBE3A gene. Maternal Ube3a deficiency (Ube3a
m-/p+), as well as complete loss of Ube3a expression (Ube3a
m-/p-), have been reproduced in the mouse model used here.

Results
Here we asked if two characteristic AS phenotypes - social-seeking behavior and hyperactivity - are reproduced in the Ube3a deficient mouse model of AS. We quantified social-seeking behavior as time spent in close proximity to a stranger mouse and activity as total time spent moving during exploration, movement speed and total length of the exploratory path. Mice of all three genotypes (Ube3am+/p+, Ube3a
m-/p+, Ube3a
m-/p-) were tested and found to spend the same amount of time in close proximity to the stranger, indicating that Ube3a deficiency in mice does not result in increased social seeking behavior or social dis-inhibition. Also, Ube3a deficient mice were hypoactive compared to their wild-type littermates as shown by significantly lower levels of activity, slower movement velocities, shorter exploratory paths and a reduced exploratory range.

Conclusions
Although hyperactivity and social-seeking behavior are characteristic phenotypes of Angelman Syndrome in humans, the Ube3a deficient mouse model does not reproduce these phenotypes in comparison to their wild-type littermates. These phenotypic differences may be explained by differences in the size of the genetic defect as ~70% of AS patients have a deletion that includes several other genes surrounding the UBE3A locus.