bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Immunity to Lethal Acute or Chronic Type IIToxoplasma gondiiInfection Is Effectively Induced in Genetically Susceptible C57BL/6 Mice by Immunization with an Attenuated Type I Vaccine Strain
Authors: Gigley Jason P. , Fox Barbara A. , Bzik David J. 
Published: September 2009

ABSTRACTC57BL/6 (B6) mice are genetically highly susceptible to chronic type IIToxoplasma gondiiinfections that invariably cause lethal toxoplasmic encephalitis. We examined the ability of an attenuated type I vaccine strain to elicit long-term immunity to lethal acute or chronic type II infections in susceptible B6 mice. Mice immunized with the type Icps1-1vaccine strain were not susceptible to a lethal (100-cyst) challenge with the type II strain ME49. Immunized mice challenged with 10 ME49 cysts exhibited significant reductions in brain cyst and parasite burdens compared to naive mice, regardless of the route of challenge infection. Remarkably,cps1-1strain-immunized B6 mice chronically infected with ME49 survived for at least 12 months without succumbing to the chronic infection. Potent immunity to type II challenge infections persisted for at least 10 months after vaccination. While thecps1-1strain-elicited immunity did not prevent the establishment of a chronic infection or clear established brain cysts,cps1-1strain-elicited CD8+immune T cells significantly inhibited recrudescence of brain cysts during chronic ME49 infection. In addition, we show that uracil starvation of thecps1-1strain induces early markers of bradyzoite differentiation. Collectively, these results suggest that more effective immune control of chronic type II infection in the genetically susceptible B6 background is established by vaccination with the nonreplicating type I uracil auxotrophcps1-1strain.
FINITE ELEMENT SIMULATION OF A NANO-SCRATCH TEST OF BONE
Authors: PARUCHURU SATYA PRASAD , WANG XIAODU 
Published: September 2009

Quality of bone tissue deteriorates with age and disease. Mechanical techniques that evaluate properties of cadaver bone help in understanding mechanisms behind aging and disease and by extension in the quality assurance of engineered bone tissue. Use of inverse engineering methods help in interpreting bone properties from experimental data. Correlation of these properties to noninvasive or minimally invasive measurements aids in assessment of the quality and fracture risk of live bone tissue. A pilot study on different age groups has shown that the removal energy dissipated per volume during the scratch may be a representative of the toughness of bone. A 3D finite element model was proposed to perform numerical simulation of bone scratch tests in order to aid in formulation of a quantitative scratch approach and assessment of in-situ properties by inverse engineering methods. Finite element modeling procedures for simulation of bone scratch test were developed. Simulation of scratch test was carried out using contact analysis. The results of finite element simulation were compared with experimental data. The simulation gave a preliminary understanding of deformation produced in the bone scratch test.
On a Simple Empirical Parameterization of Topography-Catalyzed Diapycnal Mixing in the Abyssal Ocean
Authors: Decloedt Thomas , Luther Douglas S. 
Published: September 2009

Abstract
The global spatial distribution of the turbulent diapycnal diffusivity in the abyssal ocean is reexamined in light of the growing body of microstructure data revealing bottom-intensified turbulent mixing in regions of rough topography. A direct and nontrivial implication of the observed intensification is that the diapycnal diffusivity Kρ, is depth dependent and patchily distributed horizontally across the world’s oceans. Theoretical and observational studies show that bottom-intensified mixing is dependent upon a variety of energy sources and processes whose contributions to mixing are sufficiently complex that their physical parameterization is premature; only rudimentary parameterizations of tidally induced mixing have been attempted, although the tides likely provide no more than half of the mechanical energy available for diapycnal mixing in the abyssal ocean. Here, an empirical (and still rudimentary) parameterization of the spatially variable mean diffusivity Kρ based on a large collection of microstructure data from several oceanic regions, is provided. The parameterization, called the roughness diffusivity model (RDM), depends only on seafloor roughness and height above bottom and has the advantage of tacitly including a broad range of mixing processes catalyzed by the roughness or acuteness of the bottom topography. The study focuses in particular on the vertical structure of Kρ and shows that exponential decay, prominent in current diapycnal mixing parameterizations, does not provide an adequate representation of the mean vertical profile. Instead, an inverse square law decay with a scale height and maximum near-boundary value depending on topographic roughness is shown to provide a more realistic vertical structure. Resulting basin-averaged diffusivities based on the RDM, which increase from ∼3 × 10−5 m2 s−1 at 1-km depth to ∼1.5 × 10−4 m2 s−1 at 4 km, are roughly consistent with spatial averages derived from hydrographic data inversions, supporting the contention that strong, localized mixing plays a major role in maintaining the observed abyssal stratification. The power required to sustain the stratification in the abyssal ocean (defined as 40°S–48°N, 1–4-km depth) is shown to be sensitive to the spatial distribution of the mixing. The power consumption in this domain, given the parameterized bottom-intensified and horizontally heterogeneous diffusivity structure in the RDM, is estimated as approximately 0.37 TW (TW = 1012 W), considerably less than the canonical value of ∼2 TW estimated under the assumption of a uniform diffusivity of ∼10−4 m2 s−1 in the abyssal ocean.
The Melting of Ice in the Arctic Ocean: The Influence of Double-Diffusive Transport of Heat from Below
Authors: Turner J. S. 
Published: September 2009

Abstract
This investigation was originally prompted by two oceanographic observations: an increased rate of melting of sea ice in the Arctic Ocean, and the advance of an anomalously warm tongue of Atlantic water intruding across the Arctic below the halocline over the past few decades. A series of laboratory model experiments has previously been carried out to explore the possibility that the extra heating at depth could be responsible for the enhanced melting rate. These experiments have demonstrated that a one-dimensional heat flux from below through a series of double-diffusive layers can in principle lead to faster melting of floating ice. However, it is now essential to test these ideas quantitatively under ocean conditions and to compare the results with other possible mechanisms of melting.
A simple calculation shows that there is enough heat in the intruding Atlantic water to melt all the ice in the Arctic in a few years if all the heat could be brought to the surface in this time. The vertical double-diffusive transport of heat is slower than this, but it is large enough to make a substantial contribution to the increased rate of melting over the last three or four decades. Another proposed mechanism for melting is the solar input to the surface mixed layer from the atmosphere. In particular years when detailed measurements and calculations have been made, this atmospheric input can explain both the seasonal cyclic behavior of ice and the increased melting rate. Given the large heat content in the intruding Atlantic layer, however, it seems worth exploring further other advective two-dimensional mechanisms that could transport this heat upward more rapidly than the purely vertical double-diffusive convection. For example, dense salty water produced by freezing on the shelves around the Arctic Basin could flow down the slope and penetrate through the halocline, thus mixing with the warm water and bringing it to the surface.
Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset
Authors: Tittarelli Andrés , Santiago Margarita , Morales Andrea , Meisel Lee A , Silva Herman 
Published: September 2009

Abstract

Background
Cold acclimation is the process by which plants adapt to the low, non freezing temperatures that naturally occur during late autumn or early winter. This process enables the plants to resist the freezing temperatures of winter. Temperatures similar to those associated with cold acclimation are also used by the fruit industry to delay fruit ripening in peaches. However, peaches that are subjected to long periods of cold storage may develop chilling injury symptoms (woolliness and internal breakdown). In order to better understand the relationship between cold acclimation and chilling injury in peaches, we isolated and functionally characterized cold-regulated promoters from cold-inducible genes identified by digitally analyzing a large EST dataset.

Results
Digital expression analyses of EST datasets, revealed 164 cold-induced peach genes, several of which show similarities to genes associated with cold acclimation and cold stress responses. The promoters of three of these cold-inducible genes (Ppbec1, Ppxero2 and Pptha1) were fused to the GUS reporter gene and characterized for cold-inducibility using both transient transformation assays in peach fruits (in fruta) and stable transformation in Arabidopsis thaliana. These assays demonstrate that the promoter Pptha1 is not cold-inducible, whereas the Ppbec1 and Ppxero2 promoter constructs are cold-inducible.

Conclusion
This work demonstrates that during cold storage, peach fruits differentially express genes that are associated with cold acclimation. Functional characterization of these promoters in transient transformation assays in fruta as well as stable transformation in Arabidopsis, demonstrate that the isolated Ppbec1 and Ppxero2 promoters are cold-inducible promoters, whereas the isolated Pptha1 promoter is not cold-inducible. Additionally, the cold-inducible activity of the Ppbec1 and Ppxero2 promoters suggest that there is a conserved heterologous cold-inducible regulation of these promoters in peach and Arabidopsis. These results reveal that digital expression analyses may be used in non-model species to identify candidate genes whose promoters are differentially expressed in response to exogenous stimuli.
NMDA Receptor Subunit Expression and PAR2 Receptor Activation in Colospinal Afferent Neurons (CANs) during Inflammation Induced Visceral Hypersensitivity
Authors: Suckow Shelby K , Caudle Robert M 
Published: September 2009

Background Visceral hypersensitivity is a clinical observation made when diagnosing patients with functional bowel disorders. The cause of visceral hypersensitivity is unknown but is thought to be attributed to inflammation. Previously we demonstrated that a unique set of enteric neurons, colospinal afferent neurons (CANs), co-localize with the NR1 and NR2D subunits of the NMDA receptor as well as with the PAR2 receptor. The aim of this study was to determine if NMDA and PAR2 receptors expressed on CANs contribute to visceral hypersensitivity following inflammation. Recently, work has suggested that dorsal root ganglion (DRG) neurons expressing the transient receptor potential vanilloid-1 (TRPV1) receptor mediate inflammation induced visceral hypersensitivity. Therefore, in order to study CAN involvement in visceral hypersensitivity, DRG neurons expressing the TRPV1 receptor were lesioned with resiniferatoxin (RTX) prior to inflammation and behavioural testing. Results CANs do not express the TRPV1 receptor; therefore, they survive following RTX injection. RTX treatment resulted in a significant decrease in TRPV1 expressing neurons in the colon and immunohistochemical analysis revealed no change in peptide or receptor expression in CANs following RTX lesioning as compared to control data. Behavioral studies determined that both inflamed non-RTX and RTX animals showed a decrease in balloon pressure threshold as compared to controls. Immunohistochemical analysis demonstrated that the NR1 cassettes, N1 and C1, of the NMDA receptor on CANs were up-regulated following inflammation. Furthermore, inflammation resulted in the activation of the PAR2 receptors expressed on CANs. Conclusion Our data show that inflammation causes an up-regulation of the NMDA receptor and the activation of the PAR2 receptor expressed on CANs. These changes are associated with a decrease in balloon pressure in response to colorectal distension in non-RTX and RTX lesioned animals. Therefore, these data suggest that CANs contribute to visceral hypersensitivity during inflammation.
Transcription factor Sp1 induces ADAM17 and contributes to tumor cell invasiveness under hypoxia
Authors: Szalad Alexandra , Katakowski Mark , Zheng Xuguang , Jiang Feng , Chopp Michael 
Published: September 2009

Abstract

Background
Expression of the Sp1 transcription factor is induced by hypoxia, and the ADAM17 promoter contains predicted Sp1 binding sites. ADAM17 contributes to hypoxic-induce invasiveness of glioma. In this study, we investigated whether Sp1 transcription factor induces ADAM17 and/or contributes to tumor cell invasiveness in hypoxia.

Methods
Employing RT-PCR and Western blot, we examined the role of Sp1 in ADAM17 transcription/expression under normoxic and hypoxic conditions, and whether it binds to the ADAM17 GC-rich promoter region using a chromatin immunoprecipitation assay. Additionally, we tested the effect of Sp1 suppression in tumor cell invasion and migration, using Matrigel basement membrane invasion chambers, a scratch wound-healing assay, and small interfering RNA.

Results
Here, we found that Sp1 binds to the ADAM17 promoter, and that Sp1 regulates ADAM17 expression under hypoxia. Furthermore, suppression of Sp1 decreases invasiveness and migration in U87 tumor cells.

Conclusion
Our findings suggest the Sp1 transcription factor mediates ADAM17 expression under hypoxia, regulates glioma invasiveness, and thus, may be a target for anti-invasion therapies.
Many LINE1 elements contribute to the transcriptome of human somatic cells
Authors: Rangwala Sanjida H , Zhang Lili , Kazazian Haig H 
Published: September 2009

Abstract
Background
While LINE1 (L1) retroelements comprise nearly 20% of the human genome, the majority are thought to have been rendered transcriptionally inactive, due to either mutation or epigenetic suppression. How many L1 elements 'escape' these forms of repression and contribute to the transcriptome of human somatic cells? We have cloned out expressed sequence tags corresponding to the 5' and 3' flanks of L1 elements in order to characterize the population of elements that are being actively transcribed. We also examined expression of a select number of elements in different individuals.

Results
We isolated expressed sequence tags from human lymphoblastoid cell lines corresponding to 692 distinct L1 element sites, including 410 full-length elements. Four of the expression tagged sites corresponding to full-length elements from the human specific L1Hs subfamily were examined in European-American individuals and found to be differentially expressed in different family members.

Conclusions
A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer and Central Nervous System Metastases
Authors: Leyland-Jones Brian 
Published: September 2009

Purpose To determine the incidence, outcomes, and current strategies for management of brain metastases in patients with human epidermal growth factor receptor 2 (HER2)–positive breast cancer. Methods A literature review was performed to obtain data on central nervous system metastases in patients with breast cancer. Results HER2 amplification/overexpression is a prognostic and predictive factor for the development of CNS metastases. Autopsy data show that the incidence rate for CNS metastases in patients with breast cancer is approximately 30%; this may be higher (ie, 30% to 50%) in patients with HER2-positive disease. Treatment with trastuzumab is not associated with an increased incidence of CNS metastases. Data from three phase III adjuvant trials showed the incidence was similar between patients who received trastuzumab and those who did not. Furthermore, trastuzumab can significantly improve overall survival in HER2-positive patients who already have CNS metastases compared with patients who do not receive trastuzumab or those who have HER2-negative brain metastases. This survival advantage is conferred via systemic control of the disease. The current standard of care for patients with CNS metastases is whole-brain radiotherapy (WBRT), with or without surgery, or stereotactic radiosurgery. In the future, novel therapies or combinations of therapies may additionally improve survival in these patients. Conclusion The incidence of CNS metastases in trastuzumab-treated patients is similar to that in all patients with HER2-positive disease. Trastuzumab can improve survival in patients with HER2-positive disease with CNS metastases.
Vasomotor Symptoms, Adoption of a Low-Fat Dietary Pattern, and Risk of Invasive Breast Cancer: A Secondary Analysis of the Women's Health Initiative Randomized Controlled Dietary Modification Trial
Authors: Caan Bette J. , Aragaki Aaron , Thomson Cynthia A. , Stefanick Marcia L. , Chlebowski Rowan , Hubbell F. Allan , Tinker Lesley , Vitolins Mara , Rajkovic Aleksandar , Bueche Maria , Ockene Judy 
Published: September 2009

Purpose To assess whether the effect of a low-fat dietary pattern on breast cancer incidence varied by report of baseline vasomotor symptoms. Methods Postmenopausal women age 50 to 79 years enrolled onto the Women's Health Initiative (WHI) Dietary Modification trial from 1993 to 1998 were randomly assigned to a low-fat dietary intervention (n = 19,541) or comparison (n = 29,294). Presence of vasomotor symptoms at baseline was ascertained from a 34-item self-report symptom inventory. Women were queried semi-annually for a new diagnosis of breast cancer. Each case report was verified by medical record and pathology report review by centrally trained WHI physician adjudicators. Results Among participants who reported hot flashes (HFs) at baseline (n = 3,375), those assigned to the low-fat diet had a breast cancer rate of 0.27 compared with their counterparts in the control group who had a rate of 0.41 (hazard ratio [HR] = 0.65; 95% CI, 0.42 to 1.01). Among women reporting no HFs (n = 45,160), the breast cancer rate was 0.42 in those assigned to the low-fat diet compared with 0.46 in the control group (HR = 0.93; 95% CI, 0.84 to 1.03; P for interaction = .12 by HF status). Furthermore, the dietary benefits observed seemed to be specific to estrogen receptor (ER) –positive/progesterone receptor (PR) –positive tumors (ER positive/PR positive v other, P for risk = .03). Although women with and without HFs differed with regard to breast cancer risk factors, the effect of the diet intervention on breast cancer incidence by HF status was consistent across risk factor strata. Conclusion The results of this trial, which are hypothesis generating, suggest that HFs may identify a subgroup of postmenopausal women whose risk of invasive breast cancer might be reduced with the adoption of a low-fat eating pattern.
Effects of Tamoxifen and Raloxifene on Memory and Other Cognitive Abilities: Cognition in the Study of Tamoxifen and Raloxifene
Authors: Legault Claudine , Maki Pauline M. , Resnick Susan M. , Coker Laura , Hogan Patricia , Bevers Therese B. , Shumaker Sally A. 
Published: September 2009

Purpose To compare the effects of two selective estrogen receptor modulators, tamoxifen and raloxifene, on global and domain-specific cognitive function. Patients and Methods The National Surgical Adjuvant Breast and Bowel Project's Study of Tamoxifen and Raloxifene (STAR) study was a randomized clinical trial of tamoxifen 20 mg/d or raloxifene 60 mg/d in healthy postmenopausal women at increased risk of breast cancer. The 1,498 women who were randomly assigned in STAR were age 65 years and older, were not diagnosed with dementia, and were enrolled onto the Cognition in the Study of Tamoxifen and Raloxifene (Co-STAR) trial, beginning 18 months after STAR enrollment started. A cognitive test battery modeled after the one used in the Women's Health Initiative Study of Cognitive Aging (WHISCA) was administered. Technicians were centrally trained to administer the battery and recertified every 6 months. Analyses were conducted on all participants and on 273 women who completed the first cognitive battery before they started taking their medications. Results Overall, there were no significant differences in adjusted mean cognitive scores between the two treatment groups across visits. There were significant time effects across the three visits for some of the cognitive measures. Similar results were obtained for the subset of women with true baseline measures. Conclusion Tamoxifen and raloxifene are associated with similar patterns of cognitive function in postmenopausal women at increased risk of breast cancer. Future comparisons between these findings and patterns of cognitive function in hormone therapy and placebo groups in WHISCA should provide additional insights into the effects of tamoxifen and raloxifene on cognitive function in older women.
Percolation Threshold of Water in Ideal Binary Mixture
Authors: Oleinikova Alla , Brovchenko Ivan 
Published: September 2009

Abstract
Percolation transitions of water and solute molecules in an ideal completely miscible aqueous solution are studied by computer simulations. Three concentration ranges with different kinds of water and solute clustering can be distinguished. An infinite water network, present in pure liquid water, breaks at some solute concentration. Accordingly, the infinite network of solute molecules, present in pure liquid solute, breaks upon addition of water. At ambient and high temperatures, there is a concentration range were both components are below their respective percolation thresholds and there are no water or solute infinite networks. The existence of such concentration range is a characteristic of a completely miscible binary mixture. Upon supercooling, the threshold concentrations decrease and simultaneous existence of the infinite networks of water and of solute becomes possible. The presence of two inter-penetrating infinite networks of molecules may be one of the conditions required for the liquid-liquid transition of one-component isotropic fluid.
Mechanical Stability of Ionotropic Alginate Beads
Authors: Degen Patrick , Leick Sabine , Rehage Heinz 
Published: September 2009

Abstract
In a series of experiments we measured the mechanical properties of single alginate beads by means of squeezing experiments between two parallel plates. We used multivalent counter-ions as cross-linking molecules for the formation of three dimensional alginate gels. In this article we examined pure Fe(II) (ferric), Fe(III) (ferrous) and Ca(II) (calcium) ions as cross-linking agents and different mixtures between these charged compounds. The results of squeezing experiments showed that capsules formed with pure ferrous ions were less stable than particles which were cross-linked with calcium or ferric ions. It turned out that at equal molar concentrations calcium and ferrous ions formed stronger gels than ferric ions. In addition to squeezing capsule experiments we also investigated different particles by optical microscopy and scanning electron microscopy. Experiments of Energy-dispersive X-ray spectroscopy (EDAX) show different compositions of these beads.