bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing anterior cingulate activation in chronic schizophrenia: a group and single‐subject fMRI study
Authors: Harrison B. J. , Yücel M. , Fornito A. , Wood S. J. , Seal M. L. , Clarke K. , Pantelis C. 
Published: February 2007

Objective:  Functional abnormalities of the dorsal anterior cingulate (dAC) region have been emphasized in schizophrenia, particularly in relation to cognitive deficits. In this study, we sought to further evaluate the notion of dAC hypofunction in chronic schizophrenia patients using a cognitive task specifically designed to activate this region, enabling both group and single‐subject level analyses.Method:  Twelve male schizophrenia patients and 14 male healthy subjects were studied with functional magnetic resonance imaging (fMRI) and the multi‐source interference task (MSIT). Patients and healthy subjects were matched for age, gender, education, task performance and gross surface morphology of the AC region. fMRI analyses were conducted at the group and single‐subject levels using stringent whole‐brain activation thresholds.Results:  Multi‐source interference task performance was associated with large and significant activation of the dAC and supplementary motor area (SMA) in patients and healthy subjects. Standard comparison of the two groups indicated that the patients were comparable with healthy subjects in their dAC activation, but had a small cluster of greater SMA activation, while single‐subject analyses identified minimal differences in the magnitude or spatial dispersion of dAC activation between the groups.Conclusion:  These findings challenge existing notions of impaired dAC activation in chronic schizophrenia and suggest that the functional pathophysiology of this medial‐wall region should be considered beyond straightforward models of hypoactivation.
Modeling Natural Attenuation with Source Control at a Chlorinated Solvents Dry Cleaner Site
Authors: Ling Meng , Rifai Hanadi S. 
Published: February 2007

AbstractA ground water flow and solute transport model was developed for a site contaminated with chlorinated solvents to simulate the site remediation activities that included natural attenuation and source control. MODFLOW was used to model the flow field, and RT3D was employed to simulate the sequential decay reactions involving perchloroethene, trichloroethene, dichloroethene, and vinyl chloride (VC). Predictive simulations were completed for two conditions: natural attenuation alone and source excavation followed by natural attenuation. Results demonstrated the feasibility of site remediation for both conditions with the latter one occurring in a shorter time frame. A detailed sensitivity analysis was performed to assess the uncertainty in model predictions. The most sensitive model parameters (i.e., initial contaminant concentrations, reaction rate constants, and source release rates) were perturbed and combined to form a number of parameter sets for use in the predictive simulations. The maximum plume length, the maximum plume concentration, and the persistence time for the noncompliance plume area were assessed to identify the possible failure scenarios and the most likely future plume configuration. Results indicated that further VC plume expansion or migration beyond site boundaries is unlikely.
Zero‐Valent Iron Emplacement in Permeable Porous Media Using Polymer Additions
Authors: Oostrom M. , Wietsma T.W. , Covert M.A. , Vermeul V.R. 
Published: February 2007

AbstractAt the Hanford Site in Washington, an extensive in situ redox manipulation (ISRM) permeable reactive barrier was installed to prevent chromate from reaching the Columbia River. However, chromium has been detected in several wells, indicating a premature loss of the reductive capacity in the aquifer. One possible cause for premature chromate breakthrough is associated with the presence of high‐permeability zones in the aquifer. The potential emplacement of zero‐valent iron (Fe0) into high‐permeability Hanford sediments to enhance the barrier’s reductive capacity using shear‐thinning fluids containing polymers was investigated in three‐dimensional wedge‐shaped aquifer models. Porous media were packed in the wedge‐shaped flow cell to create either a heterogeneous layered system with a high‐permeability zone between two low‐permeability zones or a high‐permeability channel surrounded by low‐permeability materials. The injection flow rate, polymer type, polymer concentration, and injected pore volumes were determined based on preliminary short‐ and long‐column experiments. The flow cell experiments indicated that iron concentration enhancements of at least 0.6% w/w could be obtained using moderate flow rates and injection of 30 pore volumes. The aqueous pressure increased by a maximum of 25 kPa during infiltration, but a decrease in permeability was not observed. Under optimal conditions, the 0.6% amended Fe0 concentration would provide approximately 20 times the average reductive capacity that is provided by the dithionite‐reduced Fe(II) in the ISRM barrier.
Optimization of Radioimmunotherapy of Solid Tumors: Biological Impediments and Their Modulation
Authors: Jain Maneesh , Venkatraman Ganesh , Batra Surinder K. 
Published: February 2007

Abstract
In contrast to the overwhelming success of radiolabeled antibodies in treating hematologic malignancies, only modest success has been achieved in the radioimmunotherapy of solid tumors. One of the major limitations in successful application of radioimmunotherapy is the large molecular size of the intact immunoglobulin that results in prolonged serum half-life and poor tumor penetration and uptake. With the advent of antibody engineering, small molecular weight antibody fragments exhibiting improved pharmacokinetics and tumor penetration have been generated. However, their clinical application has been limited by suboptimal tumor uptake and short tumor residence time. There is a greater realization that optimization of the molecular size of the antibodies alone is not sufficient for clinical success of radioimmunotherapy. In addition to their size, radiolabeled antibodies encounter other impediments before reaching their target antigens expressed on the cell surface of solid tumors. Some of the barriers include poor blood flow in large tumors, permeability of vascular endothelium, elevated interstitial fluid pressure of tumor stroma, and heterogeneous antigen expression. Recent research has considerably improved our understanding and appreciation of these forces, and the new wave of optimization strategies involves the use of biological modifiers to modulate the impediments posed by solid tumors. In combination with radiolabeled antibodies, various agents are being used to improve the tumor blood flow, enhance vascular permeability, lower tumor interstitial fluid pressure by modulating stromal cells and extracellular matrix components, up-regulate the expression of target antigens, and improve the penetration and retention of the radiopharmaceuticals. This review outlines ongoing research efforts involving biological modifiers to optimize the uptake and efficacy of radiolabeled antibodies for the treatment of solid tumors.
Concepts of Motor Learning Applied to a Rehabilitation Protocol Using Biofeedback to Improve Gait in a Chronic Stroke Patient: An A-B System Study With Multiple Gait Analyses
Authors: Jonsdottir Johanna , Cattaneo Davide , Regola Alberto , Crippa Alessandro , Recalcati Mauro , Rabuffetti Marco , Ferrarin Maurizio , Casiraghi Anna 
Published: February 2007

Objective. The impact of electromyographic biofeedback (EMG BFB) applied during functional gait activities and employed in accord with theories on motor learning was investigated in a chronic hemiplegic patient. Methods. A single-subject A-B design was used. EMG BFB was applied to the triceps surae during gait. A rehabilitation program with a fading frequency of BFB application and an increasing variability in the task training was implemented. Responses to the rehabilitation program were documented via multiple quantitative gait analyses, performed during a baseline, treatment, and at follow-up 6 weeks after the end of treatment. Results.From baseline to end of treatment, there were significant changes in ankle power at push-off, both in amplitude and timing, as well as onset of ankle power at push-off relative to heel strike of the healthy leg. There was a significant increase in gait velocity, step length of the healthy side, stride length, and stride frequency. At follow-up, changes were still significantly different from baseline and the patient had reduced the use of the cane in activities of daily living. Conclusions. BFB appears to have been effective in promoting positive changes in gait in this pilot study. The rehabilitation protocol also appeared to be effective in promoting learning and the incorporation of trained activities into daily activities.
Musculoskeletal Adaptations in Chronic Spinal Cord Injury: Effects of Long-term Soleus Electrical Stimulation Training
Authors: Shields Richard K. , Dudley-Javoroski Shauna 
Published: February 2007

Objective. The purpose of this study was to determine whether long-term electrical stimulation training of the paralyzed soleus could change this muscle’s physiological properties (torque, fatigue index, potentiation index, torque-time integral) and increase tibia bone mineral density. Methods. Four men with chronic (>2 years) complete spinal cord injury (SCI; American Spinal Injury Association classification A) trained 1 soleus muscle using an isometric plantar flexion electrical stimulation protocol. The untrained limb served as a within-subject control. The protocol involved ~ 30 minutes of training each day, 5 days a week, for a period of 6 to 11 months. Mean compliance over 11 months of training was 91% for 3 subjects. A fourth subject achieved high compliance after only 5 months of training. Mean estimated compressive loads delivered to the tibia were ~110% of body weight. Over the 11 months of training, the muscle plantar flexion torque, fatigue index, potentiation index, and torque-time integral were evaluated periodically. Bone mineral density (dual-energy x-ray absorptiometry) was evaluated before and after the training program. Results.The trained limb fatigue index, potentiation index, and torque-time integral showed rapid and robust training effects ( P <.05). Soleus electrical stimulation training yielded no changes to the proximal tibia bone mineral density, as measured by dual-energy x-ray absorptiometry. The subject with low compliance experienced fatigue index and torque-time integral improvements only when his compliance surpassed 80%. In contrast, his potentiation index showed adaptations even when compliance was low. Conclusions. These findings highlight the persistent adaptive capabilities of chronically paralyzed muscle but suggest that preventing musculoskeletal adaptations after SCI may be more effective than reversing changes in the chronic condition.
Embryonic sympathoblasts transiently express TrkB in vivo and proliferate in response to brain-derived neurotrophic factor in vitro
Authors: Straub Jennifer A , Sholler Giselle L Saulnier , Nishi Rae 
Published: February 2007

Abstract

Background
Nerve growth factor and neurotrophin-3 are involved in the development of sympathetic neurons; however, whether brain derived neurotrophic factor also plays a role is not known. The purpose of this study was to determine whether BDNF and its receptor, TrkB, are expressed during the development of paravertebral sympathetic ganglia in vivo and to determine the effect of BDNF in vitro.

Results
As neural crest cells coalesce to form sympathetic ganglia, TrkB-positive cells are seen in both chicken and mouse embryos. In chicken embryos, TrkB-expressing cells first appear at Hamburger-Hamilton Stage (St) 27 and they co-express HNK-1, confirming that they are migrating neural crest cells. The TrkB-positive cells lack neural markers at this stage; however, they migrate with other neurally differentiating cells that are TrkA and TrkC-positive. By St. 29/30, TrkB-positive cells begin to express the neural specific markers Hu C/D and Islet-1; eventually, all TrkB positive cells commence neural differentiation. By St. 34, TrkB and TrkC staining are lost. BDNF transcript expression parallels that of TrkB. In the mouse, TrkB-positive cells surround newly formed sympathetic ganglia and a small number of TrkB positive cells that co-express tyrosine hydroxylase are seen within ganglia between E13.5-15. In cell culture, many cells from St. 29–30 chicken lumbar sympathetic ganglia express neural markers and are dividing, indicating that they are sympathoblasts. Sympathoblasts and neurons require both nerve growth factor and neurotrophin-3 for survival. BDNF increases the number of cells expressing neural markers in culture by increasing number of cells that incorporate bromodeoxyuridine. In contrast, most TrkB-positive sympathetic cells in vivo are not actively proliferating between E6–E8.

Conclusion
Developing paravertebral sympathetic ganglia in avian and murine embryos contain a subpopulation of sympathoblasts that transiently express TrkB and ultimately commence neuronal differentiation. These TrkB expressing sympathoblasts are not actively dividing in vivo; yet, when placed in vitro, will divide in response to BDNF. This suggests that the availability of BDNF in vivo fails to reach a threshold necessary to induce proliferation. We suggest that excess TrkB stimulation of sympathoblasts in vivo may lead to the genesis of neuroblastoma.
Wnt signaling induces differentiation of progenitor cells in organotypic keratinocyte cultures
Authors: Slavik Marni A , Allen-Hoffmann B Lynn , Liu Bob Y , Alexander Caroline M 
Published: February 2007

Abstract

Background
Interfollicular skin develops normally only when the activity of the progenitor cells in the basal layer is counterbalanced by the exit of cells into the suprabasal layers, where they differentiate and cornify to establish barrier function. Distinct stem and progenitor compartments have been demonstrated in hair follicles and sebaceous glands, but there are few data to describe the control of interfollicular progenitor cell activity. Wnt signaling has been shown to be an important growth-inducer of stem cell compartments in skin and many other tissues.

Results
Here, we test the effect of ectopic Wnt1 expression on the behavior of interfollicular progenitor cells in an organotypic culture model, and find that Wnt1 signaling inhibits their growth and promotes terminal differentiation.

Conclusion
These results are consistent with the phenotypes reported for transgenic mice engineered to have gain or loss of function of Wnt signaling in skin, which would recommend our culture model as an accurate one for molecular analysis. Since it is known that canonical ligands are expressed in skin, it is likely that this pathway normally regulates the balance of growth and differentiation, and suggests it could be important to pathogenesis.
Phosphorylation of ERK in Neurokinin 1 Receptor-Expressing Neurons in Laminae III and IV of the Rat Spinal Dorsal Horn Following Noxious Stimulation
Authors: Polgár Erika , Campbell Annie D , MacIntyre Lynsey M , Watanabe Masahiko , Todd Andrew J 
Published: February 2007

Background: There is a population of large neurons with cell bodies in laminae III and IV of the spinal dorsal horn which express the neurokinin 1 receptor (NK1r) and have dendrites that enter the superficial laminae. Although it has been shown that these are all projection neurons and that they are innervated by substance P-containing (nociceptive) primary afferents, we know little about their responses to noxious stimuli. In this study we have looked for phosphorylation of extracellular signal-regulated kinases (ERKs) in these neurons in response to different types of noxious stimulus applied to one hindlimb of anaesthetised rats. The stimuli were mechanical (repeated pinching), thermal (immersion in water at 52°C) or chemical (injection of 2% formaldehyde). Results: Five minutes after each type of stimulus we observed numerous cells with phosphorylated ERK (pERK) in laminae I and IIo, together with scattered positive cells in deeper laminae. We found that virtually all of the lamina III/IV NK1r-immunoreactive neurons contained pERK after each of these stimuli and that in the great majority of cases there was internalisation of the NK1r on the dorsal dendrites of these cells. In addition, we also saw neurons in lamina III that were pERK-positive but lacked the NK1r, and these were particularly evident in animals that had had the pinch stimulus. Conclusion: Our results demonstrate that lamina III/IV NK1r-immunoreactive neurons show receptor internalisation and ERK phosphorylation after mechanical, thermal or chemical noxious stimuli.
Dynamics of in silico leukocyte rolling, activation, and adhesion
Authors: Tang Jonathan , Ley Klaus F , Hunt C Anthony 
Published: February 2007

AbstractBackgroundWe present a multilevel, agent based, in silico model that represents the dynamics of rolling, activation, and adhesion of individual leukocytes in vitro. Object-oriented software components were designed, verified, plugged together, and then operated in ways that represent the molecular and cellular mechanisms believed responsible for leukocyte rolling and adhesion. The result is an in silico analogue of an experimental in vitro system. The experimentally measured, phenotypic attributes of the analogue were compared and contrasted to those of leukocytes in vitro from three different experimental conditions.ResultsThe individual in silico dynamics of "rolling" on simulated P-selectin, and separately on simulated VCAM-1, were an acceptable match to individual in vitro distance-time and velocity-time measurements. The analogues are also able to represent the transition from rolling to adhesion on P-selectin and VCAM-1 in the presence of GRO-α chemokine. The individual in silico and in vitro behavioral similarities translated successfully to population level measures. These behavioral similarities were enabled in part by subdividing the functionality of the analogue's surface into 600 independent, "cell"-controlled, equally capable modules of comparable functionality.ConclusionThe overlap in phenotypic attributes of our analogue with those of leukocytes in vitro confirm the considerable potential of our model for studying the key events that determine the behavioral outcome of individual leukocytes during rolling, activation, and adhesion. Our results provide an important foundation and framework for future in silico research into plausible causal links between well-documented, subcellular molecular level events and the variety of systemic phenotypic attributes that distinguish normal leukocyte adhesion from abnormal disease-associated adhesion.
Early onset pauciarticular arthritis is the major risk factor for naproxen-induced pseudoporphyria in juvenile idiopathic arthritis
Authors: Schäd Susanne G , Kraus Andrea , Haubitz Imme , Trcka Jiri , Hamm Henning , Girschick Hermann J 
Published: February 2007

Abstract
Pseudoporphyria (PP) is characterized by skin fragility, blistering and scarring in sun-exposed skin areas without abnormalities in porphyrin metabolism. The phenylpropionic acid derivative group of nonsteroidal anti-inflammatory drugs, especially naproxen, is known to cause PP. Naproxen is currently one of the most prescribed drugs in the therapy of juvenile idiopathic arthritis (JIA). The prevalence of PP was determined in a 9-year retrospective study of children with JIA and associated diseases. In addition, we prospectively studied the incidence of PP in 196 patients (127 girls and 69 boys) with JIA and associated diseases treated with naproxen from July 2001 to March 2002. We compared these data with those from a matched control group with JIA and associated diseases not treated with naproxen in order to identify risk factors for development of PP. The incidence of PP in the group of children taking naproxen was 11.4%. PP was particularly frequent in children with the early-onset pauciarticular subtype of JIA (mean age 4.5 years). PP was associated with signs of disease activity, such as reduced haemoglobin (<11.75 g/dl), and increased leucocyte counts (>10,400/μl) and erythocyte sedimentation rate (>26 mm/hour). Comedications, especially chloroquine intake, appeared to be additional risk factors. The mean duration of naproxen therapy before the onset of PP was 18.1 months, and most children with PP developed their lesions within the first 2 years of naproxen treatment. JIA disease activity seems to be a confounding factor for PP. In particular, patients with early-onset pauciarticular JIA patients who have significant inflammation appear to be prone to developing PP upon treatment with naproxen.
Induction of epithelial to mesenchymal transition in PMC42-LA human breast carcinoma cells by carcinoma-associated fibroblast secreted factors
Authors: Lebret Stephanie C , Newgreen Donald F , Thompson Erik W , Ackland M Leigh 
Published: February 2007

Abstract
Background
Breast carcinoma is accompanied by changes in the acellular and cellular components of the microenvironment, the latter typified by a switch from fibroblasts to myofibroblasts.

Methods
We utilised conditioned media cultures, Western blot analysis and immunocytochemistry to investigate the differential effects of normal mammary fibroblasts (NMFs) and mammary cancer-associated fibroblasts (CAFs) on the phenotype and behaviour of PMC42-LA breast cancer cells. NMFs were obtained from a mammary gland at reduction mammoplasty, and CAFs from a mammary carcinoma after resection.

Results
We found greater expression of myofibroblastic markers in CAFs than in NMFs. Medium from both CAFs and NMFs induced novel expression of α-smooth muscle actin and cytokeratin-14 in PMC42-LA organoids. However, although conditioned media from NMFs resulted in distribution of vimentin-positive cells to the periphery of PMC42-LA organoids, this was not seen with CAF-conditioned medium. Upregulation of vimentin was accompanied by a mis-localization of E-cadherin, suggesting a loss of adhesive function. This was confirmed by visualizing the change in active β-catenin, localized to the cell junctions in control cells/cells in NMF-conditioned medium, to inactive β-catenin, localized to nuclei and cytoplasm in cells in CAF-conditioned medium.

Conclusion
We found no significant difference between the influences of NMFs and CAFs on PMC42-LA cell proliferation, viability, or apoptosis; significantly, we demonstrated a role for CAFs, but not for NMFs, in increasing the migratory ability of PMC42-LA cells. By concentrating NMF-conditioned media, we demonstrated the presence of factor(s) that induce epithelial-mesenchymal transition in NMF-conditioned media that are present at higher levels in CAF-conditioned media. Our in vitro results are consistent with observations in vivo showing that alterations in stroma influence the phenotype and behaviour of surrounding cells and provide evidence for a role for CAFs in stimulating cancer progression via an epithelial-mesenchymal transition. These findings have implications for our understanding of the roles of signalling between epithelial and stromal cells in the development and progression of mammary carcinoma.
DarkHorse: a method for genome-wide prediction of horizontal gene transfer
Authors: Podell Sheila , Gaasterland Terry 
Published: February 2007

AbstractA new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. The method is quantitative, reproducible, and computationally undemanding. It can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. The method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or unavailable. These features are demonstrated in bacterial, archaeal, and eukaryotic examples.