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PubMed2004

Novel nuclear defects in KLP61F-deficient mutants in Drosophila are partially suppressed by loss of Ncd function.

KLP61F in Drosophila and other BimC kinesins are essential for spindle bipolarity across species; loss of BimC function generates high frequencies of monopolar spindles. Concomitant loss of Kar3 kinesin function increases the frequency of bipolar spindles although the underlying mechanism is not known. Recent studies raise the question of whether BimC kinesins interact with a non-microtubule spindle matrix rather than spindle microtubules. Here we present cytological evidence that loss of KLP61F function generates novel defects during M-phase in the organization and integrity of the nuclear lamina, an integral component of the nuclear matrix. Larval neuroblasts and spermatocytes of klp61F mutants showed deep involutions in the nuclear lamina extending toward the centrally located centrosomes. Repositioning of centrosomes to form monopolar spindles probably does not cause invaginations as similar invaginations formed in spermatocytes lacking centrosomes entirely. Immunofluorescence microscopy indicated that non-claret disjunctional (Ncd) is a component of the nuclear matrix in somatic cells and spermatocytes. Loss of Ncd function increases the frequency of bipolar spindles in klp61F mutants. Nuclear defects were incompletely suppressed; micronuclei formed near telophase at the poles of bipolar spindle in klp61F ncd spermatocytes. Our results are consistent with a model in which KLP61F prevents Ncd-mediated collapse of a nonmicrotubule matrix derived from the interphase nucleus.

Animals↗

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↗

PubMed2005

Automated variance reduction for MCNP using deterministic methods.

In order to reduce the user's time and the computer time needed to solve deep penetration problems, an automated variance reduction capability has been developed for the MCNP Monte Carlo transport code. This new variance reduction capability developed for MCNP5 employs the PARTISN multigroup discrete ordinates code to generate mesh-based weight windows. The technique of using deterministic methods to generate importance maps has been widely used to increase the efficiency of deep penetration Monte Carlo calculations. The application of this method in MCNP uses the existing mesh-based weight window feature to translate the MCNP geometry into geometry suitable for PARTISN. The adjoint flux, which is calculated with PARTISN, is used to generate mesh-based weight windows for MCNP. Additionally, the MCNP source energy spectrum can be biased based on the adjoint energy spectrum at the source location. This method can also use angle-dependent weight windows.

Algorithms↗

PubMedDate not supplied

Real-time harmonic contrast material-specific US of focal liver lesions.

Recent advances in contrast material-enhanced ultrasonography (US) mainly include (a) development of low-acoustic-pressure (low-mechanical-index) harmonic software, capable of obtaining real-time images without disrupting contrast material microbubbles, and (b) commercialization of new contrast media ("second-generation" contrast media), capable of producing intense echo signals in this low-mechanical-index setting. With use of low-mechanical-index continuous-mode contrast-enhanced US, the circulatory kinetic models of various focal liver lesions can be displayed dynamically. Hepatic lesions usually have typical perfusion characteristics and enhancement patterns through the various phases of parenchymal enhancement, which helps characterize lesions and, in most cases, allows definitive diagnosis, even among lesions that exhibit very similar baseline appearances. Because of the use of harmonic technologies at low emission frequencies, there is some loss of spatial resolution and overall image quality, typically resulting in a grainy appearance. In addition, lesion depth affects the detectability of vascularity to some degree in that poor signal arises from deep-seated lesions. Moreover, liver attenuation (eg, in patients with steatosis or chronic liver disease) further reduces the sensitivity of contrast-enhanced US. Nevertheless, with its unique capacity to provide images in real time, low-mechanical-index contrast-enhanced US is the dynamic imaging modality of choice in the differential diagnosis of focal liver lesions.

Adult↗

PubMed2005

The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

Rice (Oryza sativa L.) is the most important food crop in the world and a model system for plant biology. With the completion of a finished genome sequence we must now functionally characterize the rice genome by a variety of methods, including comparative genomic analysis between cereal species and within the genus Oryza. Oryza contains two cultivated and 22 wild species that represent 10 distinct genome types. The wild species contain an essentially untapped reservoir of agriculturally important genes that must be harnessed if we are to maintain a safe and secure food supply for the 21st century. As a first step to functionally characterize the rice genome from a comparative standpoint, we report the construction and analysis of a comprehensive set of 12 BAC libraries that represent the 10 genome types of Oryza. To estimate the number of clones required to generate 10 genome equivalent BAC libraries we determined the genome sizes of nine of the 12 species using flow cytometry. Each library represents a minimum of 10 genome equivalents, has an average insert size range between 123 and 161 kb, an average organellar content of 0.4%-4.1% and nonrecombinant content between 0% and 5%. Genome coverage was estimated mathematically and empirically by hybridization and extensive contig and BAC end sequence analysis. A preliminary analysis of BAC end sequences of clones from these libraries indicated that LTR retrotransposons are the predominant class of repeat elements in Oryza and a roughly linear relationship of these elements with genome size was observed.

Base Sequence↗

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↗

PubMed2006

Novel multi-depth microfluidic chip for single cell analysis.

A novel multi-depth microfluidic chip was fabricated on glass substrate by use of conventional lithography and three-step etching technology. The sampling channel on the microchip was 37 microm deep, while the separation channel was 12 microm deep. A 1mm long weir was constructed in the separation channel, 300 microm down the channel crossing. The channel at the weir section was 6 microm deep. By using the multi-depth microfluidic chip, human carcinoma cells, which easily aggregate, settle and adhere to the surface of the channel, can be driven from the sample reservoir to the sample waste reservoir by hydrostatic pressure generated by the difference of liquid level between sample and sample waste reservoirs. Single cell loading into the separation channel was achieved by applying a set of pinching potentials at the four reservoirs. The loaded cell was stopped by the weir and precisely positioned within the separation channel. The trapped cell was lysed by sodium dodecyl sulfate (SDS) containing buffer solution in 20s. This approach reduced the lysing time and improved the reproducibility of chip-based electrophoresis separations. Reduced glutathione (GSH) and reactive oxygen species (ROS) were used as model intracellular components in single human carcinoma cells, and the constituents were separated by chip-based electrophoresis and detected by laser-induced fluorescence (LIF). A throughput of 15 samples/h, a migration time precision of 3.1% RSD for ROS and 4.9% RSD for GSH were obtained for 10 consecutively injected cells.

Fluorescence↗

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↗

PubMed2004

[Men of science in Brazil: colonial empires and the circulation of information (1780-1810)].

In the eighteenth century, the Portuguese imperial model yielded to other international strategies, organized according to a logic of networks that revolved around centers for the production of knowledge and the creation and redistribution of scientific products. Within this context, Portugal underwent a 'conversion' that drew it towards the French and British colonial systems. A self-legitimized scientific field was one of the corollaries of the European Enlightenment, a process that involved at least two generations of men of science and, most importantly, whose success relied on the engagement of the State. This process did not transpire systemactically in Brazil, although many of the country's men of science were well abreast of the Enlightenment's most modern philosophical and scientific theories. Policies to foster scientific activities in Brazil did not occur in tandem with broad, deep transformations in the spheres of administration, sociability, institutions, economics, or culture.

Brazil↗

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↗

PubMed2006

Dopamine-dependent non-linear correlation between subthalamic rhythms in Parkinson's disease.

The basic information architecture in the basal ganglia circuit is under debate. Whereas anatomical studies quantify extensive convergence/divergence patterns in the circuit, suggesting an information sharing scheme, neurophysiological studies report an absence of linear correlation between single neurones in normal animals, suggesting a segregated parallel processing scheme. In 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated monkeys and in parkinsonian patients single neurones become linearly correlated, thus leading to a loss of segregation between neurones. Here we propose a possible integrative solution to this debate, by extending the concept of functional segregation from the cellular level to the network level. To this end, we recorded local field potentials (LFPs) from electrodes implanted for deep brain stimulation (DBS) in the subthalamic nucleus (STN) of parkinsonian patients. By applying bispectral analysis, we found that in the absence of dopamine stimulation STN LFP rhythms became non-linearly correlated, thus leading to a loss of segregation between rhythms. Non-linear correlation was particularly consistent between the low-beta rhythm (13-20 Hz) and the high-beta rhythm (20-35 Hz). Levodopa administration significantly decreased these non-linear correlations, therefore increasing segregation between rhythms. These results suggest that the extensive convergence/divergence in the basal ganglia circuit is physiologically necessary to sustain LFP rhythms distributed in large ensembles of neurones, but is not sufficient to induce correlated firing between neurone pairs. Conversely, loss of dopamine generates pathological linear correlation between neurone pairs, alters the patterns within LFP rhythms, and induces non-linear correlation between LFP rhythms operating at different frequencies. The pathophysiology of information processing in the human basal ganglia therefore involves not only activities of individual rhythms, but also interactions between rhythms.

Adult↗