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PubMed2004

Simulation of the regional manifestation of asthma.

Asthma presents serious medical problems of global proportions. Clinical data suggest that the disease occurs preferentially at regions designated by large (0 </= I </= 5), central (6 </= I </= 11), and small (12 </= I </= 16) airways, where I defines branching generations within lungs. Our straightforward hypothesis, therefore, was that the efficacies of pharmacologic drugs proposed for the treatment and prophylaxis of asthma would be enhanced via their targeted delivery to appropriate sites. Hence, we have developed a mathematical model describing the behavior and fate of inhaled aerosols. Original algorithms have been derived to detail the physical manifestation of asthma as distinct components of smooth muscle constriction and inflammation. We have conducted a systematic analysis of the relative effects of morphology, ventilation, and particle size on aerosol deposition. Different intensities of asthma were simulated by reducing airway diameters by prescribed amounts. To show the real clinical applications of modeling, we have also simulated the performance of a popular nebulizer. Regarding therapeutic implications, it is clear that disease-induced changes in airway morphologies have pronounced effects on the administration of inhaled drugs. Likewise, ventilation affects both the total aerosol mass deposited and its relative spatial distribution among airways. By formulating these effects, the computer code allows drugs (e.g., bronchodilators for constriction, steroids for inflammation) to be selectively deposited. We suggest, therefore, that the code can be used in a complementary manner with clinical studies and can be integrated into aerosol therapy regimens.

Aerosols↗
PubMed2006

Antifungal prophylaxis in liver transplant patients: a systematic review and meta-analysis.

We performed a meta-analysis to determine whether antifungal prophylaxis decreases infectious morbidity and mortality in liver transplant patients. We searched for randomized trials dealing with prophylaxis with systemic antifungal agents. We used a fixed effect model, with risk ratio (RR) and 95% confidence interval (CI); we assessed study quality for heterogeneity and publication bias. Six studies (5 double-blind), for a total of 698 patients, compared fluconazole, itraconazole, or liposomal amphotericin to placebo (5 studies) or oral nystatin. Prophylaxis reduced colonization (RR, 0.45; CI, 0.37-0.55), total proven fungal infections (RR, 0.31; CI, 0.21-0.46), which included both superficial (RR, 0.27; CI, 0.16-0.45) and invasive (RR, 0.33; CI, 0.18-0.59) infections, and mortality attributable to fungal infection (RR, 0.30; CI, 0.12-0.75). Prophylaxis did not affect overall mortality (RR, 1.06; CI, 0.69-1.64) or empiric treatment for suspected fungal infection (RR, 0.80; CI, 0.39-1.67). The beneficial effect of antifungal prophylaxis was predominantly associated with the reduction of Candida albicans infection and mortality attributable to C. albicans. Compared to controls, however, patients receiving prophylaxis experienced a higher proportion of episodes of non-albicans Candida, and in particular of C. glabrata. No beneficial effect on invasive Aspergillus infection was observed. In conclusion, our analysis shows a clear, though limited, beneficial effect of antifungal prophylaxis in liver transplant patients. Concerns about the selection of triazole-resistant Candida strains, however, are realistic, and the potential disadvantages of prophylaxis should be weighed against the established benefits.

Antifungal Agents↗
PubMed2004

Kinetics of myc-max-mad gene expression during hepatocyte proliferation in vivo: Differential regulation of mad family and stress-mediated induction of c-myc.

Mad proteins (Mad1, Mxi1, Mad3, Mad4, Mnt/Rox) are biochemical and biological antagonists of c-Myc oncoprotein. Mad-Max dimers repress the transcription of the same target genes activated by Myc-Max dimers. Despite the critical role of Max and Mad proteins as modulators of c-Myc functions, there are no comparative data on their regulation in vivo. We carried out a systematic analysis of c-myc, max, and mad family expression in a model of synchronized cell proliferation in vivo in adult tissues, that is, rat hepatocytes after partial hepatectomy. We confirmed the previously reported early peak of c-myc expression after hepatectomy but we show that it did not correlate with hepatocyte proliferation as it also occurred in sham-operated animals as a result of surgical stresses. A second peak of c-myc expression was observed later, at the time of the wave of DNA synthesis. No such expression was detected in sham-operated rat quiescent hepatocytes. max expression increased around 4-16 h after hepatectomy, before the peaks of c-myc and DNA synthesis. mxi1 and mad4 were slightly downregulated during liver regeneration. mnt/rox expression did not change. These expression patterns suggest a role of Myc-Max for efficient mitogenic response of hepatocytes. We also analyzed the effects of Myc and Max ectopic expression on the clonogenic growth of the rat hepatoma cells. Expression of c-Myc and Max increased clonogenic growth, whereas the reduction of c-Myc levels by an antisense vector decreased growth. The results suggest nonredundant roles for mad genes in hepatocyte proliferation and point to c-Myc as a putative target for anticancer therapy of liver cancer.

Animals↗
PubMed2005

Metal artifacts caused by gradient switching.

In metal parts, e.g., implants or instruments, eddy currents can be induced from gradient switching if positioned off-center inside the MR scanner. For the first time, a systematic analysis of related artifacts was performed. Current strength increases in conjunction with increasing size of the part, increasing electrical conductivity, distance from isocenter, and increasing gradient strengths. A xy-plane oriented copper ring (d(o) = 20 mm, d(i) = 15 mm, 2 mm thick) was examined at isocenter and at x = 15 cm, y = z = 0. Comparisons of xy-, xz-, and yz-slices, recorded for both possibilities to select encoding directions, revealed effects from ramp-down of the slice-selection and ramp-up of the read-out gradient. Near the metal part, temporary inhomogeneities were superimposed to the static field and spin-dephasing signal loss resulted, despite using spin-echo technique. Artifacts depended on excitation and read-out bandwidth. For an equivalent titanium ring, conductivity related effects could not be ascertained but distinct susceptibility effects occurred. MR compatibility of implants/instruments therefore requires both low susceptibility and low conductivity.

Artifacts↗
PubMed2002

Multiphoton stimulation of neurons.

We pulsed the activation of neurons using a femtosecond laser. Pyramidal neurons are depolarized and fire action potentials when high intensity mode-locked infrared light irradiates somatic membranes and axon initial segments. This depolarization is reversible, does not occur with CW laser light, and appears to be due to multiphoton excitation. We describe two regimes of multiphoton optical stimulation. Low intensity, long duration laser irradiation produces a sustained depolarization, insensitive to sodium channel blockers yet sensitive to antioxidants. On the other hand, high intensity, short duration irradiation can induce fast depolarizations, which appear due to different mechanism. The combination of multiphoton stimulation and optical probing could enable systematic analysis of circuits.

Action Potentials↗
PubMed1995

Neuronal control of leech swimming.

Leech swimming is produced by the antiphasic contractions of dorsal and ventral longitudinal muscles that travel rearward along the animal and propel it forward. Research over the past three decades has focused on identifying the underlying neuronal circuit and mechanisms that produce and control this coordinated movement pattern. Investigations have also tested whether leech swimming is modifiable, both by experience and by neuromodulators. One outcome has been the identification of several functional classes of neurons associated with swimming. Systematic analysis of the interactions between these neurons had led to the elucidation of a neuronal circuit that adequately accounts for the generation of the swim motor program cord. The swim motor program appears to be produced by a chain of coupled segmental oscillators whose intrinsic properties and intersegmental connections ensure the coordinated expression of swimming along the nerve cord. In addition, neurons identified in the head ganglion comprise two parallel, but opposite-acting, systems that control the initiation of swimming in response to sensory input. Also, the pathway by which body wall stimulation initiates swimming shows a simple form of learning, that is habituation. Repeatedly stroking the leech body wall decreases both the probability of initiating swimming and the length of elicited swim episodes. Finally, the biogenic amine serotonin, which is found in the nerve cord, affects leech swimming in a number of ways. Serotonin's modulation of swimming is due, in part, to its effect of the membrane properties of swim-initiating interneurons and several swim motor neurons.

Animals↗
PubMed2006

PIK3CA mutation and histological type in breast carcinoma: high frequency of mutations in lobular carcinoma.

Mutations in the PIK3CA gene have recently been reported in different human neoplasms, including breast cancer. This paper reports the results of a systematic analysis of PIK3CA mutations in different histological types of breast carcinoma. One hundred and eighty invasive breast carcinomas, comprising 74 ductal, 56 lobular, 22 mucinous, 20 medullary, and eight papillary, were selected on the basis of their histological type in a consecutive series of 780 breast cancers. Exons 1-20 of the PIK3CA gene were subjected to SSCP analysis followed by direct sequencing. PIK3CA mutations were observed in 46 (26%) of the 180 tumours examined: 23 (50%) mutations were located in exon 9, and 23 (50%) in exon 20. Mutations were frequent in lobular (46%), less frequent in ductal (22%), and uncommon in medullary (10%), mucinous (5%), and papillary tumours (12%) (p = 0.0002). Mutations in exon 9 were more frequent in lobular carcinomas (30% of cases) than in the other histological types (less than 5% of cases) (p = 0.00014). No significant differences were observed in the distribution of mutations in exon 20. There was no significant correlation between PIK3CA mutations and other clinicopathological and biological variables, including age, tumour size, lymph node metastases, oestrogen receptor (ER) status, progesterone receptor (PgR) status, p53 gene mutations, and p53 protein expression. The findings indicate that in invasive breast carcinomas, PIK3CA alterations are mainly present in lobular and ductal tumours, whereas the other histological types, known to be associated with a favourable prognosis, show a very low incidence of PIK3CA mutations.

Aged↗
PubMed2005

Role of heat treatment in childhood cancers: distinct resistance profiles of solid tumor cell lines towards combined thermochemotherapy.

BACKGROUND: Since information on the efficacy of hyperthermia in combination with chemotherapy on pediatric tumors is limited, we performed a systematic analysis on the synergistic effects of a combined application of heat and chemotherapy on 20 tumor cell lines derived from patients with neuroblastomas, Ewing tumors, germ cell tumors (GCT), and osteosarcomas. METHODS: Cisplatin (cDDP), a cross-linking agent, and etoposide (VP-16), a topoisomerase II inhibitor, were examined either alone or in combination with heat (42 degrees C, 43 degrees C) by using the XTT-assay 1. RESULTS: Our data demonstrate that heat stress at 43 degrees C for 1 hr, but not at 42 degrees C, leads to a notable cytotoxic effect on the different tumor cells. The comparison of mean survival fractions reveals values between 62% for neuroblastoma cells and 76% for Ewing tumor cells. Analyzing the sensitivity to chemotherapy alone, our results show that cDDP (5 microg/ml) reduces cell growth to 47% in Ewing tumor cells, to 61% in neuroblastoma cells, to 75% in GCT cells, and to 76% in osteosarcoma cells. Treatment with VP-16 (10 microg/ml) decreases cell survival to mean values between 58% (neuroblastomas) and 77% (osteosarcomas). Simultaneous application of heat and chemotherapy enhances synergistically cDDP cytotoxicity in all tumor types tested, whereas the efficacy of VP-16 is only slightly influenced by additional application of hyperthermia. The cytotoxicity of cDDP (5 microg/ml) can be increased by a factor of between 1.5 and 2.5 at 42 degrees C and from 2.6 to 14.0 at 43 degrees C. Furthermore, the results show that the sensitivity to heat (43 degrees C) as well as the sensitivity to chemotherapy and combined thermochemotherapy varies considerably between cell lines of the same tumor group. CONCLUSIONS: Simultaneous application of hyperthermia synergistically enhances the cytotoxicity of the alkylating agent cDDP, but not of the topoisomerase II inhibitor VP-16, in a defined spectrum of cell lines from different pediatric tumor entities.

Antineoplastic Agents↗
PubMed2006

Development and research in idiopathic thrombocytopenic purpura: an inflammatory and autoimmune disorder.

Bleeding and isolated thrombocytopenia in idiopathic thrombocytopenic purpura (ITP) are phenomena of a transient or long-term disturbed immune response. Since 1980, ITP has become a model for targeted therapeutic immunomodulation with still unclear mechanisms of action. The systematic analysis of ITP aims to determine more clearly defined patient subgroups for targeted therapy and to explore the complex immune disturbances in this autoimmune disorder.

Autoimmune Diseases↗
PubMed2006

Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness.

High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4-5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology".

Algorithms↗
PubMed2006

Pitfalls in non-therapeutic research in children.

Research has brought significant medical advances in modern times benefiting virtually all people. Children as a class should not be excluded from research studies. However, non-therapeutic research is potentially problematic in children because they must be afforded special protection from harm and exploitation by care-givers, researchers, and institutional review boards. An article in this month's journal provides an opportunity for a systematic analysis using the methodology provided by the United States Code of Federal Regulations. The research design of this particular study does not appear to stand up to the requirements of the Code.

Biopsy↗
PubMed2026

The Multi-Omics Landscape of Enzymatic Alterations in Systemic Lupus Erythematosus.

OBJECTIVE: Systemic lupus erythematosus (SLE) is an autoimmune disease closely associated with enzyme dysfunction, yet its underlying molecular mechanisms remain incompletely understood. This study aims to characterize enzyme-network alterations associated with SLE status and disease activity and to identify candidate molecules with potential clinical relevance. METHODS: We integrated proteomic and phosphoproteomic data from peripheral blood mononuclear cells (PBMCs) of 130 SLE patients and 90 healthy controls (HC), along with transcriptomic data from 1461 SLE patients. Through systematic analysis of key enzyme phosphorylation sites, upstream transcription factors (TFs), and computationally prioritized candidate compounds, we sought to characterize enzyme-centered regulatory associations. RESULTS: Integrated proteomic and phosphoproteomic analyses revealed significant metabolic and signaling pathway disturbances, along with distinct phosphorylation patterns in SLE immune cells. Multiple SLE-associated and disease-activity-associated candidate molecules were identified. Regulatory network analysis uncovered an upstream transcription factor cluster centered around STAT1. Computational drug screening identified computationally prioritized candidate compounds with multi-gene DSigDB associations, which require further clinical safety evaluation and experimental validation. CONCLUSIONS: This study constructs a molecular map of SLE, highlighting associations between enzyme-network alterations, catalytic dysregulation, and SLE-related immune molecular signatures, and identifies candidate molecules for future clinical and functional evaluation.

Humans↗
PubMed2002

Inhibition of orthotopic growth and metastasis of androgen-sensitive human prostate tumors in mice by bioactive soybean components.

BACKGROUND: Systematic analysis of the influence of diet on the initiation and progression of prostate cancer is often difficult in human populations, for which dietary variables overlap a diversity of genetic backgrounds and social behaviors. Animal models that emulate human prostate cancer allow experimental analysis of the mechanisms of action of nutritional agents that show anti-prostate cancer activity. METHODS: We have used an orthotopic implant model to characterize the in vivo response of androgen-sensitive LNCaP prostate tumors to three well-characterized soy dietary supplements: isoflavone depleted soy protein, soy phytochemical concentrate (SPC), and genistin. RESULTS: In male SCID mice orthotopically implanted with the androgen-sensitive human prostate cell line LNCaP, dietary supplements of soy protein, genistin, and SPC reduced primary tumor weight by 42% (P = 0.07), 57% (P < 0.05) and 70% (P < 0.005), respectively. All three soy supplements significantly increased tumor apoptosis and decrease microvessel density, with no significant change in tumor proliferation. Each supplement produced a distinct serum androgen response, with genistin producing the greatest decrease in total serum testosterone and dihydrotestosterone (DHT) (P < 0.05) and the greatest increase in testosterone to DHT ratio (P < 0.05) and soy protein the greatest decrease in bioactive androgen (P < 0.05). Only SPC significantly inhibited metastases to lymph nodes and lungs, and only SPC produced a significant increase in tumor p53 expression. CONCLUSION: Taken together, these data suggest that the anti-prostate cancer activity of dietary soy protein, soy phytochemicals, and genistin use different molecular pathways. In addition, we have demonstrated that this animal model can be used in the design of dietary strategies for prostate cancer prevention and therapy.

Animals↗
PubMed2005

Magnetic fluid hyperthermia (MFH)reduces prostate cancer growth in the orthotopic Dunning R3327 rat model.

BACKGROUND: Magnetic fluid hyperthermia (MFH) is a new technique for interstitial hyperthermia or thermoablation based on AC magnetic field-induced excitation of biocompatible superparamagnetic nanoparticles. Preliminary studies in the Dunning tumor model of prostate cancer have demonstrated the feasibility of MFH in vivo. To confirm these results and evaluate the potential of MFH as a minimally invasive treatment of prostate cancer we carried out a systematic analysis of the effects of MFH in the orthotopic Dunning R3327 tumor model of the rat. METHODS: Orthotopic tumors were induced by implantation of MatLyLu-cells into the prostates of 48 male Copenhagen rats. Animals were randomly allocated to 4 groups of 12 rats each, including controls. Treatment animals received two MFH treatments following a single intratumoral injection of a magnetic fluid. Treatments were carried out on days 10 and 12 after tumor induction using an AC magnetic field applicator system operating at a frequency of 100 kHz and a variable field strength (0--18 kA/m). On day 20, animals were sacrificed and tumor weights in the treatment and control groups were compared. In addition, tumor growth curves were generated and histological examinations and iron measurements in selected organs were carried out. RESULTS: Maximum intratumoral temperatures of over 70 degrees C could be obtained with MFH at an AC magnetic field strength of 18 kA/m. At a constant field strength of 12.6 kA/m, mean maximal and minimal intratumoral temperatures recorded were 54.8 degrees C (centrally) and 41.2 degrees C (peripherally). MFH led to an inhibition of tumor growth of 44%-51% over controls. Mean iron content in the prostates of treated and untreated (injection of magnetic fluids but no AC magnetic field exposure) animals was 82.5%, whereas only 5.3% of the injected dose was found in the liver, 1.0% in the lung, and 0.5% in the spleen. CONCLUSIONS: MFH led to a significant growth inhibition in this orthotopic model of the aggressive MatLyLu tumor variant. Intratumoral deposition of magnetic fluids was found to be stable, allowing for serial MFH treatments without repeated injection. The optimal treatment schedules and temperatures for MFH need to be defined in further studies.

Animals↗
PubMed2007

TGFBR3 loss and consequences in prostate cancer.

BACKGROUND: Resistance to transforming growth factor-beta (TGF-beta) is important in tumorigenesis. TGF-beta resistance mechanisms in prostate cancer are not well understood. METHODS: We have conducted a systematic analysis of TGF-beta pathway components with a meta-analysis of seven microarray studies using Oncomine and evaluated the results of TGFBR3 expression in prostate cell lines. Furthermore, we knocked down TGFBR3 in prostate epithelial cells and analyzed the consequences of TGFBR3 knockdown. RESULTS: We found that TGFBR3 is the TGF-beta component most commonly downregulated among localized human prostate cancer studies. TGFBR3 knockdown led to focus formation and enhanced expression of CD133, a marker found on prostate cancer stem cells. DNA microarray analysis of TGFBR3 knockdown cells identified 101 genes regulated by TGFBR3. Seven of these genes show a corresponding decrease in clinical prostate cancer specimens, which include genes involved in prostate mass and vasculature. CONCLUSIONS: TGFBR3 downregulation is an important step in prostate tumorigenesis.

Blotting, Western↗
PubMed1985

Identification of prostate and other cancers by two-dimensional protein electrophoresis.

Some cancers are so undifferentiated as to preclude their identification, and this hinders selection of an appropriate therapy. The systematic analysis and cataloguing of electrophoresed proteins from identified cancers and their comparison with the protein patterns from histologically indeterminate cancers should provide a general means of identifying the latter.

Adenocarcinoma↗
PubMed2004

Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.

In several crystal structures of 3-phosphoglycerate kinase (PGK), the two domains occupy different relative positions. It is intriguing that the two extreme (open and closed) conformations have never been observed for the enzyme from the same species. Furthermore, in certain cases, these different crystalline conformations represent the enzyme-ligand complex of the same composition, such as the ternary complex containing either the substrate 3-phosphoglycerate (3-PG) and beta,gamma-imido-adenosine-5'-triphosphate (AMP-PNP), an analogue of the substrate MgATP, or 3-PG and the product MgADP. Thus, the protein conformation in the crystal is apparently determined by the origin of the isolated enzyme: PGK from pig muscle has only been crystallized in open conformation, whereas PGK from either Thermotoga maritima or Trypanosoma brucei has only been reported in closed conformations. A systematic analysis of the underlying sequence differences at the crucial hinge regions of the molecule and in the protein-protein contact surfaces in the crystal, in two independent pairs of open and closed states, have revealed that 1) sequential differences around the molecular hinges do not explain the appearance of fundamentally different conformations and 2) the species-specific intermolecular contacts between the nonconserved residues are responsible for stabilizing one conformation over the other in the crystalline state. A direct relationship between the steric position of the contacts in the three-dimensional structure and the conformational state of the protein has been demonstrated.

Adenosine Diphosphate↗
PubMed2006

Molecular dynamics simulation of Leishmania major surface metalloprotease GP63 (leishmanolysin).

One of the molecular factors contributing to Leishmania sp. virulence and pathogenesis is the major surface metalloprotease GP63, alternatively called leishmanolysin, MSP, and PSP (EC 3.4.24.36). Here, the molecular dynamics simulation of Leishmania major GP63 in water at pH 7 is reported. Upon solvation, GP63 undergoes a sharp structural relaxation with respect to the crystal structure. The fluctuation pattern occurs essentially in solvent-exposed nonstructured regions. By contrast, the active site turns out to be rigid. Essential dynamics and dynamic-domain analyses, both carried out on the equilibrated portion of GP63, show that the fingerprint fluctuations of GP63 are practically characterized by the motion of a large part of the N-terminal domain. These results appear to be in line with substrate recognition and (pro)enzyme activation played by the N-terminal domain of GP63. A systematic analysis among a series of 10 homologs of GP63 also shows that the residues involved in the interdomain bending result highly conserved. This finding also suggests possible relationship between the maintainance of proteolytic activity and the similarity of the dynamical properties of the related enzymes.

Animals↗