bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tissue fibrosis and carcinogenesis: Divergent or successive pathways dictate multiple molecular therapeutic targets for oligo decoy therapies
Authors: Cutroneo Kenneth R. , White Sheryl L. , Chiu Jen‐Fu , Paul Ehrlich H. 
Published: January 2006

AbstractThe extracellular matrix (ECM) is composed of several families of macromolecular components: fibrous proteins such as collagens, type I collagen (COL1), type III collagen (COL3), fibronectin, elastin, and glycoconjugates such as proteoglycans and matrix glycoproteins. Their receptors on the cell membrane, most of which in the case of the ECM belong to the integrins, which are heterodimeric proteins composed of α and β chains. COL1 is the major fibrous collagen of bone, tendon, and skin; while COL3 is the more pliable collagen of organs like liver. Focus will not only be given to the regulation of synthesis of several fibrogenic parameters but also modulation of their degradation during growth factor‐induced tissue fibrosis and cancer development. Evidence will be provided that certain tissues, which undergo fibrosis, also become cancerous. Why does there exist a divergency between tissues, which undergo frank fibrosis as an endpoint, and those tissues that undergo fibrosis and subsequently are susceptible to carcinogenicity; resulting from the etiological factor(s) causing the initial injury? For example, why does a polyvinyl alcohol (PVA) sponge implant become encapsulated and filled with fibrous tissue then fibrosis tissue growth stops? Why does the subcutaneous injection of a fibrogenic growth factor cause a benign growth and incisional wounding results in fibrosis and ultimately scarring? There are many examples of tissues, which undergo fibrosis as a prerequisite to carcinogenesis. Is there a cause‐effect relationship? If you block tissue fibrosis in these precancerous tissues, would you block cancer formation? What are the molecular targets for blocking fibrosis and ultimately carcinogenesis? How can oligo decoys may be used to attenuate carcinogenesis and which oligo decoys specifically attenuate fibrogenesis as a prelude to carcinogenesis? What are other molecular targets for oligo decoy therapy in carcinogenesis? J. Cell. Biochem. 97: 1161–1174, 2006. © 2006 Wiley‐Liss, Inc.
Force meets chemistry: Analysis of mechanochemical conversion in focal adhesions using fluorescence recovery after photobleaching
Authors: Lele Tanmay P. , Thodeti Charles K. , Ingber Donald E. 
Published: January 2006

AbstractMechanotransduction—the process by which mechanical forces are converted into changes of intracellular biochemistry—is critical for normal cell and tissue function. Integrins facilitate mechanochemical conversion by transferring physical forces from the extracellular matrix, across the cell surface, and to cytoskeletal‐associated proteins within focal adhesions. It is likely that force alters biochemistry at these sites by altering molecular binding affinities of a subset of focal adhesion proteins, but this has been difficult to quantify within living cells. Here, we describe how the fluorescence recovery after photobleaching (FRAP) technique can be adapted and used in conjunction with mathematical models to directly measure force‐dependent alterations in molecular binding and unbinding rate constants of individual focal adhesion proteins in situ. We review these recent findings, and discuss the strengths and limitations of this approach for analysis of mechanochemical signaling in focal adhesions and other cellular structures. The ability to quantify molecular binding rate constants in the physical context of the living cytoplasm should provide new insight into the molecular basis of cellular mechanotransduction. It also may facilitate future efforts to bridge biological experimentation and mathematical modeling in our quest for a systems biology level description of cell regulation. J. Cell. Biochem. 97: 1175–1183, 2006. © 2006 Wiley‐Liss, Inc.
In vivo photothermal flow cytometry: Imaging and detection of individual cells in blood and lymph flow
Authors: Zharov Vladimir P. , Galanzha Ekaterina I. , Tuchin Valery V. 
Published: January 2006

AbstractFlow cytometry is a well‐established, powerful technique for studying cells in artificial flow in vitro. This review covers a new potential application of this technique for studying normal and abnormal cells in their native condition in blood or lymph flow in vivo. Specifically, the capabilities of the label‐free photothermal (PT) technique for detecting and imaging cells in the microvessel network of rat mesentery are analyzed from the point of view of overcoming the problems of flow cytometry in vivo. These problems include, among others, the influences of light scattering and absorption in vessel walls and surrounding tissues, instability of cell velocity, and cells numbers and positions in a vessel's cross‐section. The potential applications of this new approach in cell biochemistry and medicine are discussed, including molecular imaging; studying the metabolism and pathogenesis of many diseases at a cellular level; and monitoring and quantifying metastatic and apoptotic cells, and/or their responses to therapeutic interventions (e.g., drug or radiation), in natural biological environments. J. Cell. Biochem. 97: 916–932, 2006. © 2006 Wiley‐Liss, Inc.
Effects of 24R,25‐ and 1α,25‐dihydroxyvitamin D3 on mineralizing growth plate chondrocytes
Authors: Wu L.N.Y. , Genge B.R. , Ishikawa Y. , Ishikawa T. , Wuthier R.E. 
Published: January 2006

AbstractTime‐ and dosage‐dependent effects of 1,25(OH)2D3 and 24,25(OH)2D3 on primary cultures of pre‐ and post‐confluent avian growth plate (GP) chondrocytes were examined. Cultures were grown in either a serum‐containing culture medium designed to closely mimic normal GP extracellular fluid (DATP5) or a commercially available serum‐free media (HL‐1) frequently used for studying skeletal cells. Hoechst DNA, Lowry protein, proteoglycan (PG), lactate dehydrogenase (LDH), and alkaline phosphatase (ALP) activity and calcium and phosphate mineral deposition in the extracellular matrix were measured. In preconfluent cultures grown in DATP5, physiological levels of 24,25(OH)2D3 (0.10–10 nM) increased DNA, protein, and LDH activity significantly more than did 1,25(OH)2D3 (0.01–1.0 nM). However, in HL‐1, the reverse was true. Determining ratios of LDH and PG to DNA, protein, and each other, revealed that 1,25(OH)2D3 specifically increased PG, whereas 24,25(OH)2D3 increased LDH. Post‐confluent cells were generally less responsive, especially to 24,25(OH)2D3. The positive anabolic effects of 24,25(OH)2D3 required serum‐containing GP‐fluid‐like culture medium. In contrast, effects of 1,25(OH)2D3 were most apparent in serum‐free medium, but were still significant in serum‐containing media. Administered to preconfluent cells in DATP5, 1,25(OH)2D3 caused rapid, powerful, dosage‐dependent inhibition of Ca2+ and Pi deposition. The lowest level tested (0.01 nM) caused >70% inhibition during the initial stages of mineral deposition; higher levels of 1,25(OH)2D3 caused progressively more profound and persistent reductions. In contrast, 24,25(OH)2D3 increased mineral deposition 20–50%; it required >1 week, but the effects were specific, persistent, and largely dosage‐independent. From a physiological perspective, these effects can be explained as follows: 1,25(OH)2D3 levels rise in hypocalcemia; it stimulates gut absorption and releases Ca2+ from bone to correct this deficiency. We now show that 1,25(OH)2D3 also conserves Ca2+ by inhibiting mineralization. The slow anabolic effects of 24,25(OH)2D3are consistent with its production under eucalcemic conditions which enable bone formation. These findings, which implicate serum‐binding proteins and accumulation of PG in modulating accessibility of the metabolites to GP chondrocytes, also help explain some discrepancies previously reported in the literature. J. Cell. Biochem. 98: 309–334, 2006. © 2006 Wiley‐Liss, Inc.
Expression analysis and modulation by HIV‐Tat of the tyrosine phosphatase HD‐PTP
Authors: Mariotti Massimo , Castiglioni Sara , Maier Jeanette A.M. 
Published: January 2006

AbstractThe human immunodeficiency virus type 1 Tat transactivates viral proteins and also affects the expression of eukaryotic genes. Since Tat is angiogenic, we assumed that the isolation of differentially expressed genes in Tat‐treated endothelial cells would yield insights into the molecular mechanisms of the angiogenic process. By RNA fingerprinting, we found that Tat upregulates the tyrosine phosphatase HD‐PTP mRNA in a human endothelial cell line. At the moment, little is known about HD‐PTP. We here show that HD‐PTP is highly conserved through evolution from yeast to man, and is ubiquitously distributed in adult and fetal tissues. HD‐PTP is expressed in human cell lines derived from different tumors, but the mRNA levels do not appear to correlate with the malignant phenotype of the cells. HD‐PTP mRNA was also detected in cell lines derived from tumors that develop in BKV/Tat‐transgenic mice. Interestingly, a relation exists between the amounts of secreted Tat and the levels of HD‐PTP mRNA. HD‐PTP encodes a 185‐kDa protein which is expressed in human endothelial from the umbilical cord and in human Kaposi‐spindle cells. Tat‐induction of HD‐PTP mRNA parallels only with a slight increase of the protein, which occurs after 24 and 48 h of incubation in the presence of Tat. These results suggest that HD‐PTP amounts might be regulated both at the transcriptional and post‐transcriptional levels. J. Cell. Biochem. 98: 301–308, 2006. © 2006 Wiley‐Liss, Inc.
Peptidomics: Identification and quantification of endogenous peptides in neuroendocrine tissues
Authors: Fricker Lloyd D. , Lim Jihyeon , Pan Hui , Che Fa‐Yun 
Published: January 2006

AbstractNeuropeptides perform a large variety of functions as intercellular signaling molecules. While most proteomic studies involve digestion of the proteins with trypsin or other proteases, peptidomics studies usually analyze the native peptide forms. Neuropeptides can be studied by using mass spectrometry for identification and quantitation. In many cases, mass spectrometry provides an understanding of the precise molecular form of the native peptide, including post‐translational cleavages and other modifications. Quantitative peptidomics studies generally use differential isotopic tags to label two sets of extracted peptides, as done with proteomic studies, except that the Cys‐based reagents typically used for quantitation of proteins are not suitable because most peptides lack Cys residues. Instead, a number of amine‐specific labels have been created and some of these are useful for peptide quantitation by mass spectrometry. In this review, peptidomics techniques are discussed along with the major findings of many recent studies and future directions for the field. © 2006 Wiley Periodicals, Inc. Mass Spec Rev 25:327–344, 2006
Minimum‐norm reconstruction for sensitivity‐encoded magnetic resonance spectroscopic imaging
Authors: Sánchez‐González Javier , Tsao Jeffrey , Dydak Ulrike , Desco Manuel , Boesiger Peter , Paul Pruessmann Klaas 
Published: January 2006

AbstractIn this work we propose minimum‐norm reconstruction as a means to enhance the spatial response behavior in parallel spectroscopic MRI. By directly optimizing the shape of the spatial response function (SRF), the new method accounts for coil sensitivity variation across individual voxels and their side lobes. In this fashion, it mitigates the signal contamination and side‐lobe aliasing, to which previous techniques are susceptible at low resolution. Although the computational burden is higher, minimum‐norm reconstruction is shown to be feasible using an iterative algorithm. Benefits in terms of SRF shape and artifact suppression are demonstrated. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Sliding multislice (SMS): A new technique for minimum FOV usage in axial continuously moving‐table acquisitions
Authors: Fautz H.‐P. , Kannengiesser S.A.R. 
Published: January 2006

AbstractA novel technique for axial continuously moving‐table scans is described that minimizes the required extension of the scanner's field of view (FOV) along the direction of table motion (z) by applying a segmented multislice acquisition technique. Any anatomical slice is acquired by applying the same phase‐encoding steps at the same spatial positions along the scanner FOV. The full k‐space data set of any anatomical slice is collected while the slice moves through the scanner from one scan position to the next. Simultaneous acquisition of multiple slices is realized by shifting the acquisition trajectories of different slices in time. It is demonstrated how the image artifact behavior that relates to varying imaging properties along the distance the table traverses during the acquisition of any given anatomical slice can be optimized simultaneously for all images. Discontinuities between the images along the slice axis are avoided because all z‐dependent scan properties are encoded identically for all slices. Flexible spatial acquisition patterns are proposed to enable data oversampling and overlapping slice acquisitions at reduced table speeds. A framework of equations is presented by which matched parameter combinations for sliding multislice acquisitions can be applied to both single‐ and multiecho sequences. The new technique is validated on phantom and in vivo measurements using a T1‐weighted fast low‐angle shot (FLASH) sequence as well as a T2‐weighted multi‐spin‐echo sequence of variable echo train lengths. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Noninvasive detection of cuprizone induced axonal damage and demyelination in the mouse corpus callosum
Authors: Sun Shu‐Wei , Liang Hsiao‐Fang , Trinkaus Kathryn , Cross Anne H. , Armstrong Regina C. , Song Sheng‐Kwei 
Published: January 2006

AbstractPreviously, we tested the prediction that axonal damage results in decreased axial diffusivity (λ∥) while demyelination leads to increased radial diffusivity (λ⟂). Cuprizone treatment of C57BL/6 mice was a highly reproducible model of CNS white matter demyelination and remyelination affecting the corpus callosum (CC). In the present study, six C57BL/6 male mice were fed 0.2% cuprizone for 12 weeks followed by 12 weeks of recovery on normal chow. The control mice were fed normal chow and imaged in parallel. Biweekly in vivo DTI examinations showed transient decrease of λ∥ in CC at 2–6 weeks of cuprizone treatment. Immunostaining for nonphosphorylated neurofilaments demonstrated corresponding axonal damage at 4 weeks of treatment. Significant demyelination was evident from loss of Luxol fast blue staining at 6–12 weeks of cuprizone ingestion and was paralleled by increased λ⟂ values, followed by partial normalization during the remyelination phase. The sensitivity of λ⟂ to detect demyelination may be modulated in the presence of axonal damage during the early stage of demyelination at 4 weeks of cuprizone treatment. Our results suggest that λ∥ and λ⟂ may be useful in vivo surrogate markers of axonal and myelin damage in mouse CNS white matter. Magn Reson Med, 2006. Published 2006 Wiley‐Liss, Inc.
Parallel imaging of hyperpolarized helium‐3 with simultaneous slice excitation
Authors: Teh Kevin , Lee Kuan J. , Paley Martyn N. J. , Wild Jim M. 
Published: January 2006

AbstractHyperpolarized (HP) gas imaging of the lungs is an ideal potential application for parallel imaging. This is due to the fact that there is limited scan time (breath hold of 20 s) and limited non‐renewable polarization. Reduced phase encode parallel imaging is demanding on hardware in that it requires multiple receivers. In this work, simultaneous parallel acquisition of hyperpolarized (HP) 3He images from multiple slices was demonstrated in phantoms and in vivo using a simultaneous slice excitation method, at a field strength of 1.5 T. The pulse sequence allows simultaneous acquisition of n slices per RF excitation, thus reducing the number of RF pulses needed to fully cover a given volume with multi‐slicing. Unlike conventional parallel imaging, this method does not require prior reference scan information, which would consume some of the finite longitudinal polarization in lung ventilation studies with HP gas. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Characterizing radial undersampling artifacts for cardiac applications
Authors: Peters Dana C. , Rohatgi Pratik , Botnar René M. , Yeon Susan B. , Kissinger Kraig V. , Manning Warren J. 
Published: January 2006

AbstractThe undersampled radial acquisition has been widely employed for accelerated (by a factor R = Nr/Np) cardiac imaging, but the resulting reduction in image quality has not been well characterized. This investigation presents a method of measuring these artifacts through synthetic undersampling of high SNR images (SNR ≥ 30). After validating the method in phantoms, the method was applied to a study of short‐axis, long‐axis, and coronary MRI imaging in healthy subjects. For 60 projections (60 Np), the total artifact is ∼10% for short and long‐axis imaging (R = 2.1) and ∼15% for coronary MRI (R = 3.7). For 60 Np, the SD of artifact in the region of the heart is 2% for short‐ and long‐axis imaging (R = 2.1) and 3.5% for coronary MRI (R = 3.7). The artifact content is less in the region of the heart than in the periphery. The artifact is very reproducible among subjects for standard views. A study of coronary MRI at progressively fewer projections (at constant scan time) showed that right coronary MRI images were acceptable if total artifact was <6.5% of image content (Np > 120, R = 2.1). Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Generalized self‐navigated motion detection technique: Preliminary investigation in abdominal imaging
Authors: Brau Anja C. S. , Brittain Jean H. 
Published: January 2006

AbstractPatient motion remains a primary obstacle to diagnostic image quality, especially in the abdomen, despite the existence of various motion artifact reduction techniques. This work presents a self‐navigated motion detection method that can be generalized for most pulse sequences and k‐space trajectories. Motion information is extracted directly from raw MR data, requiring no additional gradient or RF pulses, no physiologic monitoring equipment, and minimal—if any—impact on scan time. Initial feasibility results with a two‐dimensional gradient echo sequence are shown in phantom studies and in vivo volunteer abdominal studies, demonstrating the sensitivity of the method to both respiratory motion and cardiovascular pulsatility. Prospectively gated images were acquired using the self‐navigated data to synchronize image acquisition with motion. These preliminary results suggest that the self‐navigated method is a promising technique for reducing motion artifacts in clinical abdominal and cardiac applications. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Controlled aliasing in volumetric parallel imaging (2D CAIPIRINHA)
Authors: Breuer Felix A. , Blaimer Martin , Mueller Matthias F. , Seiberlich Nicole , Heidemann Robin M. , Griswold Mark A. , Jakob Peter M. 
Published: January 2006

AbstractThe CAIPIRINHA (Controlled Aliasing In Parallel Imaging Results IN Higher Acceleration) concept in parallel imaging has recently been introduced, which modifies the appearance of aliasing artifacts during data acquisition in order to improve the subsequent parallel imaging reconstruction procedure. This concept has been successfully applied to simultaneous multi‐slice imaging (MS CAIPIRINHA). In this work, we demonstrate that the concept of CAIPIRINHA can also be transferred to 3D imaging, where data reduction can be performed in two spatial dimensions simultaneously. In MS CAIPIRINHA, aliasing is controlled by providing individual slices with different phase cycles by means of alternating multi‐band radio frequency (RF) pulses. In contrast to MS CAIPIRINHA, 2D CAIPIRINHA does not require special RF pulses. Instead, aliasing in 2D parallel imaging can be controlled by modifying the phase encoding sampling strategy. This is done by shifting sampling positions from their normal positions in the undersampled 2D phase encoding scheme. Using this modified sampling strategy, coil sensitivity variations can be exploited more efficiently in multiple dimensions, resulting in a more robust parallel imaging reconstruction. Magn Reson Med, 2006. © 2006 Wiley‐Liss, Inc.
Cystometric and in vitro muscle studies of cystoplastic appendiceal segments in the rat
Authors: Semerdzhiev Yavor , Frederiksen Hans , Hedlund Petter , Davidsson Thomas , Mansson Wiking , Uvelius Bengt 
Published: January 2006

AbstractAimsThe functional integration of the smooth muscle of enterocystoplasties into the detrusor muscle was investigated in an awake‐rat cystometry model and in vitro.MethodsThe upper fourth of the bladder was removed, and a detubularized appendiceal segment (7 × 7 mm), with preserved vasculature, was incorporated into the bladder. After 1 or 3 months, a catheter was fixed to the top of the bladders. After a 3‐day recovery, cystometries were performed. In separate experiments, agonist and nerve‐induced responses were evaluated on isolated bladder strips.ResultsCystometries revealed reduced basal pressure and micturition pressure in enterocystoplasty (ECP) bladders. Bladder capacity and micturition volume were increased. Threshold pressure (pressure immediately before micturition) was significantly lower at 1 month, but not at 3 months. Bladder compliance was significantly higher in the operated at 1 month but not at 3 months. Threshold tension did not differ between control and corresponding operated groups. Residual urine was significantly higher in the operated groups. ECP strips showed increased maximal contractions to nerve stimulation, to levels similar to those of detrusor strips. Maximal responses to carbachol increased to levels between those of intestine and detrusor. The inhibitory effect of scopolamine on nerve induced contractions increased to levels similar to those for detrusor. Purinergic activation had no effect on intestinal or ECP strips, but contracted detrusor muscle.ConclusionsThe smooth muscle of the bowel segment in rat ECP bladders underwent a partial change in the response to nerve stimulation from that of intestine towards that of detrusor. The cystometry experiments suggested a partial functional integration of the ECP segment into the detrusor. Neurourol. Urodynam. 25:259–267, 2006. © 2006 Wiley‐Liss, Inc.
Reinnervation of hair cells by auditory neurons after selective removal of spiral ganglion neurons
Authors: Martinez‐Monedero Rodrigo , Corrales C. Eduardo , Cuajungco Math P. , Heller Stefan , Edge Albert S.B. 
Published: January 2006

AbstractHearing loss can be caused by primary degeneration of spiral ganglion neurons or by secondary degeneration of these neurons after hair cell loss. The replacement of auditory neurons would be an important step in any attempt to restore auditory function in patients with damaged inner ear neurons or hair cells. Application of β‐bungarotoxin, a toxin derived from snake venom, to an explant of the cochlea eradicates spiral ganglion neurons while sparing the other cochlear cell types. The toxin was found to bind to the neurons and to cause apoptotic cell death without affecting hair cells or other inner ear cell types as indicated by TUNEL staining, and, thus, the toxin provides a highly specific means of deafferentation of hair cells. We therefore used the denervated organ of Corti for the study of neuronal regeneration and synaptogenesis with hair cells and found that spiral ganglion neurons obtained from the cochlea of an untreated newborn mouse reinnervated hair cells in the toxin‐treated organ of Corti and expressed synaptic vesicle markers at points of contact with hair cells. These findings suggest that it may be possible to replace degenerated neurons by grafting new cells into the organ of Corti. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006