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Results for “Deep generative model”

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PubMed2000

Solution structure of the interacting domains of the Mad-Sin3 complex: implications for recruitment of a chromatin-modifying complex.

Gene-specific targeting of the Sin3 corepressor complex by DNA-bound repressors is an important mechanism of gene silencing in eukaryotes. The Sin3 corepressor specifically associates with a diverse group of transcriptional repressors, including members of the Mad family, that play crucial roles in development. The NMR structure of the complex formed by the PAH2 domain of mammalian Sin3A with the transrepression domain (SID) of human Mad1 reveals that both domains undergo mutual folding transitions upon complex formation generating an unusual left-handed four-helix bundle structure and an amphipathic alpha helix, respectively. The SID helix is wedged within a deep hydrophobic pocket defined by two PAH2 helices. Structure-function analyses of the Mad-Sin3 complex provide a basis for understanding the underlying mechanism(s) that lead to gene silencing.

Amino Acid Sequence↗

PubMed1986

[OMRON RF hyperthermia treatment system HEH-500 C].

The RF capacitive type hyperthermia system "HEH-500 C" enables regional heating for superficial and deep seated tumors. It consists of a high frequency generator (frequency; 13.56 MHz, out put power; 500 watts), a control unit, a cooling unit for the applicators, an I/F unit (communicate the thermometer to RF generator and plotter printer), a thermometer (thermocouple thermometer or fiber fluorothermometer) and a plotter printer. Heating profile of HEH-500 C was presented with thermographic picture on TX-150 muscle equivalent phantom. Effects of bone and fat layer on heating profile of phantom were also examined. Points to be solved on thermometry, electromagnetic field environment and clinical use were also discussed.

Humans↗

PubMed2002

Structural biology of C1.

The classical complement pathway is a major element of innate immunity against infection, and is also involved in immune tolerance, graft rejection and various pathologies. This pathway is triggered by C1, a multimolecular protease formed from the association of a recognition protein, C1q, and a catalytic subunit, the calcium-dependent tetramer C1s-C1r-C1r-C1s, which comprises two copies of each of the modular proteases C1r and C1s. All activators of the pathway are recognized by the C1q moiety of C1, a process that generates a conformational signal that triggers self-activation of C1r, which in turn activates C1s, the enzyme that mediates specific cleavage of C4 and C2, the C1 substrates. Early work based on biochemical and electron microscopy studies has allowed characterization of the domain structure of the C1 subcomponents and led to a low-resolution model of the complex in which the elongated C1s-C1r-C1r-C1s tetramer folds into a compact, figure-of-8-shaped conformation upon interaction with C1q. The strategy used over the past decade was based on a dissection of the C1 proteins into modular segments to characterize their function and solve their three-dimensional structure by X-ray crystallography or NMR spectroscopy. This approach allows deep insights into the structure-function relationships of C1, particularly with respect to the assembly of the C1 complex and the mechanisms underlying its activation and proteolytic activity.

Animals↗

PubMed2002

Technical characterization of an ultrasound source for noninvasive thermoablation by high-intensity focused ultrasound.

OBJECTIVE: To develop a generator for high-intensity focused ultrasound (HIFU, a method of delivering ultrasonic energy with resultant heat and tissue destruction to a tight focus at a selected depth within the body), designed for extracorporeal coupling to allow various parenchymal organs to be treated. MATERIAL AND METHODS: The ultrasound generated by a cylindrical piezo-ceramic element is focused at a depth of 10 cm using a parabolic reflector with a diameter of 10 cm. A diagnostic B-mode ultrasonographic transducer is integrated into the source to allow the focus to be located in the target area. The field distribution of the sound pressure was measured in degassed water using a needle hydrophone. An ultrasound-force balance was used to determine the acoustic power. These measurements allowed the spatially averaged sound intensity to be calculated. The morphology and extent of tissue necrosis induced by HIFU was examined on an ex-vivo kidney model. RESULTS: The two-dimensional field distribution resulted in an approximately ellipsoidal focus of 32 x 4 mm (- 6 dB). The spatially maximum averaged sound intensity was 8591 W/cm2 at an electrical power of 400 W. The lesion caused to the ex-vivo kidney at this maximum generator power with a pulse duration of 2 s was a clearly delineated ellipsoidal coagulation necrosis up to 8.8 x 2.3 mm (length x width) and with central liquefied necrosis of 7.9 x 1.9 mm. CONCLUSION: This newly developed ultrasound generator with a focal length of 10 cm can induce clear necrosis in parenchymal tissue. Because of its specific configuration and the available power range of the ultrasound generator, there is potential for therapeutic noninvasive ablation of tissue deep within a patient's body.

Animals↗

PubMed2003

Regional uptake of meal fatty acids in humans.

Two protocols were performed to study meal fatty acid metabolism. In protocol 1, 14 patients scheduled for elective intra-abdominal surgery (11 undergoing bariatric surgery for severe obesity) consumed a meal containing [3H]triolein in the evening before surgery. This allowed us to measure adipose tissue lipid specific activity (SA) in mesenteric and omental, deep and superficial abdominal subcutaneous adipose tissue. Intra-abdominal adipose tissue lipid SA was greater than subcutaneous lipid SA. There were no significant differences between mesenteric and omental or between deep and superficial abdominal subcutaneous adipose tissue. In protocol 2, meal fatty acid oxidation and uptake into subcutaneous and omental adipose tissue ([3H]triolein) were measured in six normal, healthy volunteers. Meal fatty acid oxidation (3H2O generation) plus that remaining in plasma ( approximately 1%) plus uptake into upper body subcutaneous, lower body subcutaneous, and visceral fat allowed us to account for 98 +/- 6% of meal fatty acids 24 h after meal ingestion. We conclude that omental fat is a good surrogate for visceral fat and that abdominal subcutaneous fat depots are comparable with regard to meal fatty acid metabolic studies. Using [3H]triolein, we were able to account for virtually 100% of meal fatty acids 24 h after meal ingestion. These results support the meal fatty acid tracer model as a way to study the metabolic fate of dietary fat.

Adipose Tissue↗

PubMed2002

Making sense of complex phenomena in biology.

The remarkable advances in biotechnology over the past two decades have resulted in the generation of a huge amount of experimental data. It is now recognized that, in many cases, to extract information from this data requires the development of computational models. Models can help gain insight on various mechanisms and can be used to process outcomes of complex biological interactions. To do the latter, models must become increasingly complex and, in many cases, they also become mathematically intractable. With the vast increase in computing power these models can now be numerically solved and can be made more and more sophisticated. A number of models can now successfully reproduce detailed observed biological phenomena and make important testable predictions. This naturally raises the question of what we mean by understanding a phenomenon by modelling it computationally. This paper briefly considers some selected examples of how simple mathematical models have provided deep insights into complicated chemical and biological phenomena and addresses the issue of what role, if any, mathematics has to play in computational biology.

Animals↗

PubMed1988

Head phantom experiment and calculation for boron neutron capture therapy.

Head phantom experiments with various neutron beams and calculations were carried out in order to provide useful information for boron neutron capture therapy (BNCT). Thermal neutron beams for thermal neutron capture therapy were used for phantom experiments with various neutron collimator aperture sizes. The filtered beam neutrons of 24 and 144 keV generated with iron and silicon filters were also used to investigate the possible application of BNCT in the treatment of deep-seated cancers. Thermal neutron fluence and induced capture gamma dose distributions within the phantom were calculated with a transport code DOT 3.5 and compared with the experimental results. The results showed that the calculation used was consistent with the experimental results and provided useful information on BNCT. The filtered beam neutron may be very useful for the treatment of deep or widespread cancer, if there were a high power research reactor constructed for this purpose.

Brain Neoplasms↗

PubMed2002

Brainstem motor loops in the control of movement.

In recent years, the role of the area around the upper brainstem, particularly the pedunculopontine (PPN) region and the zona incerta (ZI), in the initiation and control of movement has generated much clinical interest. Using electrophysiological and pharmacological methods, we have further explored these structures and their influence in motor control in the nonhuman primate and in patients with proximal tremor. We have found that lesioning the PPN and electrical stimulation at high frequencies of the PPN region in the normal-behaving primate induces akinesia, and low frequency stimulation can induce tremor. In the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine hydrochloride (MPTP) -treated parkinsonian primate model, bicuculline, a gamma-aminobutyric acid antagonist, can alleviate akinesia when infused into the PPN region. Further studies will elucidate the possible clinical implications of these observations. The ZI has reciprocal connections with several cortical areas, the upper brainstem, cerebellum, and thalamus. We have found that chronic, high-frequency deep brain stimulation of the ZI suppresses proximal limb tremor. Field potential recordings from the ZI show significant coherence with concurrent proximal muscle electromyograms. This finding has potential clinical relevance as proximal tremor generally does not respond well to thalamic surgery and may be severely disabling.

Animals↗

PubMed2003

Investment in prolonged thromboprophylaxis with dalteparin improves clinical outcomes after hip replacement.

Clinical guidelines recommend the use of extended out-of-hospital thromboprophylaxis in patients who have had major arthroplasty. However, the cost-effectiveness of prolonging pharmacological thromboprophylaxis into the out-of-hospital phase following hip replacement surgery remains the subject of considerable debate. This debate centers on the clinical relevance of the 'surrogate' venographic endpoints that have been used in most clinical trials and used to generate some of the cost analyses of thromboprophylaxis. The objective of this study was to estimate, from the payer perspective, the direct medical costs of prolonging the duration of thromboprophylaxis with dalteparin from 1 week to 28-35 days in patients undergoing hip replacement, and to compare these to the costs associated with using 'standard' in-hospital thromboprophylaxis with low-molecular-weight heparin (LMWH) or warfarin. To derive 'best' estimates for rates of clinically and economically relevant thromboembolism associated with hip replacement surgery (i.e. those that would in reality incur management costs), we used data on the prevalence of both symptomatic and asymptomatic deep vein thrombosis (DVT) and pulmonary embolism (PE). These estimates were used in conjunction with diagnostic-related groups (DRG) reimbursement rates and a dalteparin cost model, which assumed home-based self-administration for prolonged thromboprophylaxis, to calculate overall direct medical costs of prolonged vs. in-hospital thromboprophylaxis. The management costs of the strategies evaluated were, to the nearest 1000 Euros: 465 000 Euros for in-hospital prophylaxis with LMWH; 339 000 Euros for in-hospital prophylaxis with warfarin; and 368 000 Euros for prolonged prophylaxis with dalteparin. For every 1000 patients treated, prolonging thromboprophylaxis with dalteparin from 1 to 4-5 weeks will avoid 30 clinical DVTs and 18 PEs at a saving of 2000 Euros per clinical event. Compared with in-hospital warfarin, prolonged thromboprophylaxis with dalteparin will avoid 28 DVTs and four PEs at an incremental cost-effectiveness ratio of 900 Euros per clinical event avoided. We consider that investment in prolonged thromboprophylaxis with dalteparin is justified for the improvement in clinical outcomes produced.

Arthroplasty, Replacement, Hip↗

PubMed2001

Assessing homeostasis through circadian patterns.

An organism is thought to be in a dynamic state of homeostasis when each physiological and behavioral system reaches a delicate balance within the framework of other regulatory processes. Many biological systems target specific set-point variables and generate circadian patterns. In this article, we focus on specific measurements representative of two systems, namely deep-body temperature and activity counts. We examine data collected every 30 minutes in mice, assume there are underlying circadian patterns, and extend the approach presented in Brumback and Rice (1998, Journal of the American Statistical Association 93, 961-976) in order to obtain estimates in the presence of correlated data. We then assess homeostasis using these estimates and their statistical properties.

Animals↗

PubMed1975

Human air space shapes, sizes, areas, and volumes.

The geometry of an enlarged reconstructed human acinus (i.e., a terminal bronchiole and distal airways and air spaces) was studied. Alveoli were categorized in six shapes: three-fourths of a spheroid, a slightly truncated cone, one-fourth of a spheroid, a cylindroid with a hemispherical bottom, a shallow cylindroid with a flat bottom, and a truncated deep ellipsoid. Sacs were usually either hemispheroids or shallow truncated cones. Ducts of eight generations were spheroid and gradually decreased in diameter (D) and length (L) as the generation number (z) increased. Considering the terminal bronchiole as the 15th generation and using Weibel's data for the first 10 generations, the dimensions, in mm, for z of 1-10 and 10-26 were reasonably described by D-z = 12e-(0.27-0.005z)z and L-z = 25e-0.187z. The predicted volume of the acinus at three-fourths total lung volume was 182.8 mm3, a volume equivalent to that of a sphere 7.04 mm in diameter. The reconstruction demonstrated a great increase in respiratory bronchiolar and ductal cross-sectional area and alveolar surface area, considerably more rapid than predicted by Weibel's model A.

Anthropometry↗

PubMed2025

Modeling Alternative Conformational States in CASP16.

The CASP16 Ensemble Prediction experiment assessed advances in methods for modeling proteins, nucleic acids, and their complexes in multiple conformational states. Targets included systems with experimental structures determined in two or three states, evaluated by direct comparison to experimental coordinates, as well as domain-linker-domain (D-L-D) targets assessed against statistical models from NMR and SAXS data. This paper focuses on the former class of multi-state targets. Ten ensembles were released as community challenges, including ligand-induced conformational changes, protein-DNA complexes, a trimeric protein, a stem-loop RNA, and multiple oligomeric states of a single RNA. For five targets, some groups produced reasonably accurate models of both reference states (best TM-score >0.75). However, with the exception of one protein-ligand complex (T1214), where an apo structure was available as a template, predictors generally failed to capture key structural details distinguishing the states. Overall, accuracy was significantly lower than for single-state targets in other CASP experiments. The most successful approaches generated multiple AlphaFold2 models using enhanced multiple sequence alignments and sampling protocols, followed by model quality based selection. While the AlphaFold3 server performed well on several targets, individual groups outperformed it in specific cases. By contrast, predictions for one protein-DNA complex, three RNA targets, and multiple oligomeric RNA states consistently fell short (TM-score <0.75). These results highlight both progress and persistent challenges in multi-state prediction. Despite recent advances, accurate modeling of conformational ensembles, particularly RNA and large multimeric assemblies, remains a critical frontier for structural biology.

AlphaFold2↗

PubMed1994

Pulse duration and peak intensity during focused ultrasound surgery: theoretical and experimental effects in rabbit brain in vivo.

The goal of this study was to establish the exposure parameters that will generate predictable thermally induced lesions in brain. In addition, the accuracy of a theoretical model for prediction of the lesion size was tested. To do this, 160 adult rabbits were sonicated (frequency 0.936 and 1.72 MHz) and then sacrificed at various intervals after the sonications. The results showed that predictable thermal lesions could be induced if the exposure durations were between 0.5 and 2 s. Dimensions of the necrosed tissue volume were roughly predictable by the theoretical calculations based on purely thermal effects. Shorter sonications required higher intensities (above 3700 W cm-2 at 1.72 MHz) resulting in mechanical effects with extensive vascular damage. Lesion size varied more at longer exposures (5 and 10 s), perhaps due to the increased effect of tissue perfusion. As a conclusion, focused ultrasound can be used for destruction of tissues deep in brain without causing undesirable mechanical effects, if the exposure parameters are selected properly.

Animals↗

PubMed2003

"Nonclassical" secretion of annexin A2 to the lumenal side of the enterocyte brush border membrane.

Annexin A2 is a member of the annexin family of Ca(2+)-dependent lipid binding proteins and believed to be engaged in membrane transport processes in a number of cell types. In small intestinal enterocytes, we localized annexin A2 to the brush border region, where it was found mainly on the lumenal side of the microvilli, showing an apical secretion by a "nonclassical" mechanism. In addition, annexin A2 was associated with surface-connected, deep apical tubules in the apical terminal web region and with an underlying pleiomorphic, tubulo-vesicular compartment (subapical compartment/multivesicular bodies). By subcellular fractionation, the 36 kDa full-length form of annexin A2 was approximately equally distributed between the Mg(2+)-precipitated fraction (containing intracellular and basolateral membranes) and the microvillar membrane fraction. In addition, a 33 kDa molecular form of annexin A2 was seen in the latter fraction that could be generated from the full-length annexin A2 by digestion with trypsin. Taken together, the results suggest that annexin A2 acts in exocytic apical membrane trafficking and is proteolytically cleaved in situ by pancreatic proteinases once it has become externalized to the lumenal side of the brush border membrane. On the basis of its well-known membrane fusogenic properties, we propose a model for the nonclassical membrane translocation of annexin A2.

Animals↗

PubMed1992

Ultrastructural pathology of experimental autoimmune uveitis. Quantitative evidence of activation and possible high endothelial venule-like changes in retinal vascular endothelium.

BACKGROUND: Experimental autoimmune uveitis (EAU) is a highly organ-specific autoimmune disease in which the target is the retinal photoreceptors. It is well recognized as a model of uveoretinitis in humans. The mechanisms that control the homing of sensitized lymphocytes and other leukocytes to the retina is unknown. The aim of this study was to investigate changes in the retinal vasculature that may be involved with aiding leukocyte-endothelial cell interactions and subsequent extravasation of leukocytes into the retina. EXPERIMENTAL DESIGN: Lewis rats immunized with S-antigen were used to produce EAU. The retinal vasculature was assessed by morphologic (light and electron microscopy) and morphometric techniques at various stages in the generation and course of the disease (days 3, 7, 11, 14, 21, 28 and 49 postimmunization) for evidence of endothelial cell (EC) activation and leukocyte-EC interaction. Image analysis of the retinal vessels at the electron microscopic level was performed to detect alterations in the thickness and irregularity of the EC surface, both considered to be important in lymphocyte homing in the high endothelial venules (HEVs) of lymphoid tissues. Control values were obtained from normal eyes, pertussis-only treated animals, and normal lymph node HEVs. RESULTS: The clinical and histopathologic changes in the eyes were consistent with previous descriptions of EAU and included perivasculitis, focal mononuclear infiltrate in the outer retina, and choroid with destruction of the photoreceptor outer segments and eventually loss of large portions of the outer retina. During the course of EAU, a significant proportion of retinal venules underwent both qualitative and quantitative morphologic changes including EC activation evident as increased cytoplasmic organelles, a 230% average increase in mean EC thickness, and a concomitant 4-fold increase in irregularity of the EC, that produced plump irregular EC with deep intercellular clefts. These alterations were maximal at day 21, however from day 11 onward, large numbers of lymphocytes and monocytes were observed adhering to or lodged in the clefts of plump EC, migrating through the EC cytoplasm, or lying beneath the EC. CONCLUSIONS: The characteristics acquired by the retinal venules during EAU are reminiscent of HEVs. This study suggests that tissue-specific changes in the endothelial cells of retinal venules may be responsible for the homing of S-antigen specific autoreactive lymphocytes to the target organ in this model of retinal autoimmunity.

Animals↗

PubMed2001

Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.

Leukotriene (LT) A(4) hydrolase/aminopeptidase (LTA4H) is a bifunctional zinc enzyme that catalyzes the biosynthesis of LTB4, a potent lipid chemoattractant involved in inflammation, immune responses, host defense against infection, and PAF-induced shock. The high resolution crystal structure of LTA4H in complex with the competitive inhibitor bestatin reveals a protein folded into three domains that together create a deep cleft harboring the catalytic Zn(2+) site. A bent and narrow pocket, shaped to accommodate the substrate LTA(4), constitutes a highly confined binding region that can be targeted in the design of specific anti-inflammatory agents. Moreover, the structure of the catalytic domain is very similar to that of thermolysin and provides detailed insight into mechanisms of catalysis, in particular the chemical strategy for the unique epoxide hydrolase reaction that generates LTB(4).

Amino Acid Sequence↗

PubMed1994

[Thyroid gland function and intrapulmonary temperature in tuberculosis].

The experiment on 140 albino mice examined the relationship between the pulmonary thermogenesis and the functional activity of the hypophyseal-thyroid system at different stages of pulmonary tuberculous inflammation development, during Staphylococcus-induced pneumonia, aseptic inflammation in lung tissue. Deep abnormalities of the heat-generating function of the lung were revealed just at the early periods of specific inflammation. The degree of hypothermal reactions of lung tissue correlated with the inhibition of hypophyseal-thyroidal function at all developmental stages of a tuberculous process. The changes were rather pronounced, stable and phasic. Spontaneous regression of the tuberculous process was not accompanied by recovery in the activity of the hypophyseal-thyroidal system, despite the fact that there was a clear-cut trend to normalization of pulmonary thermogenesis.

Animals↗

PubMed2000

De novo adipose tissue generation through long-term, local delivery of insulin and insulin-like growth factor-1 by PLGA/PEG microspheres in an in vivo rat model: a novel concept and capability.

This study was undertaken to characterize the duration of long-term growth factor delivery by poly(lactic-co-glycolic-acid)-polyethylene glycol (PLGA/PEG) microspheres and to evaluate the potential of long-term delivery of insulin and insulin-like growth factor-1 (IGF-1) for the de novo generation of adipose tissue in vivo. PLGA/PEG microspheres containing insulin and IGF-1, separately, were produced by a double-emulsion solvent-extraction technique. In the first phase of the experiment, the in vitro release kinetics of the microspheres were evaluated for the optical density and polyacrylamide gel electrophoresis of solutions incubated with insulin-containing microspheres for four different periods of time (n = 1). The finding of increased concentrations of soluble insulin with increased incubation time confirmed continual protein release. In the second stage of the experiment, 16 rats were divided equally into four study groups (insulin, IGF-1, insulin + IGF-1, and blank microspheres) (n = 4). Insulin and IGF-1 containing microspheres were administered directly to the deep muscular fascia of the rat abdominal wall to evaluate the potential for de novo adipose tissue generation via adipogenic differentiation from native nonadipocyte cell pools in vivo. Animals treated with blank microspheres served as an external control group. At the 4-week harvest period, multiple ectopic islands of adipose tissue were observed on the abdominal wall of the animals treated with insulin, IGF-1, and insulin + IGF-1 microspheres. Such islands were not seen in the blank microsphere group. Hematoxylin and eosin-stained sections of the growth factor groups demonstrated mature adipocytes interspersed with fibrous tissue superficial to the abdominal wall musculature and continuous with the fascia. Oil-Red-O stained sections demonstrated that these cells contained lipid. Computer-aided image analysis of histologic sections confirmed that there were statistically significant increases in the amount of "ectopic" adipose neotissue developed on the abdominal wall of animals treated with growth factor microspheres. In conclusion, this study confirms the long-term release of proteins from PLGA/PEG microspheres up to 4 weeks and demonstrates the potential of long-term local insulin and IGF-1 to induce adipogenic differentiation to mature lipid-containing adipocytes from nonadipocyte cell pools in vivo at 4 weeks.

Abdominal Muscles↗