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PubMed1980

pK determinations via pH-mobility curves obtained by isoelectric focusing-electrophoresis: theory and experimental verification.

Basic equations have been derived linking the electrophoretic migration in a stationary pH gradient of simple, singly charged cations or anions and of mono- mono- valent ampholytes with the pKs of their ionizable groups. In the case of diprotic ampholytes, an equation and a curve are described calculating a correction factor to be applied to the mobility measurements, accounting for the influence of the opposite charge species on the mobility curve of the ion being measured. This correction factor is a function of delta pK and increases exponentially with decreasing values of delta pK. These theoretical considerations have been experimentally verified by running pH-mobility curves of colored compounds, such as methyl red, neutral red and dexorubicin. The pKs thus measured were in excellent agreement with the pKs obtained independently by spectrophotometric titrations.

Ampholyte Mixtures↗

PubMed2006

Advanced approach for intraoperative MRI guidance and potential benefit for neurosurgical applications.

PURPOSE: To present an advanced approach for intraoperative image guidance in an open 0.5 T MRI and to evaluate its effectiveness for neurosurgical interventions by comparison with a dynamic scan-guided localization technique. MATERIALS AND METHODS: The built-in scan guidance mode relied on successive interactive MRI scans. The additional advanced mode provided real-time navigation based on reformatted high-quality, intraoperatively acquired MR reference data, allowed multimodal image fusion, and used the successive scans of the built-in mode for quick verification of the position only. Analysis involved tumor resections and biopsies in either scan guidance (N = 36) or advanced mode (N = 59) by the same three neurosurgeons. Technical, surgical, and workflow aspects were compared. RESULTS: The image quality and hand-eye coordination of the advanced approach were improved. While the average extent of resection, neurologic outcome after functional MRI (fMRI) integration, and diagnostic yield appeared to be slightly better under advanced guidance, particularly for the main surgeon, statistical analysis revealed no significant differences. Resection times were comparable, while biopsies took around 30 minutes longer. CONCLUSION: The presented approach is safe and provides more detailed images and higher navigation speed at the expense of actuality. The surgical outcome achieved with advanced guidance is (at least) as good as that obtained with dynamic scan guidance.

Adult↗

PubMed1991

A new device to stabilize templates for transperineal I-125 implants.

Transperineal Iodine-125 implants of the prostate are currently being performed at Memorial Sloan-Kettering Cancer Center with CT-based treatment planning and transrectal ultrasound for verification of proper needle placement in the prostate at the time of implantation. An adjustable device, the WIPI, has been designed to stabilize the perineal template and rectal obturator during planning and implementation of the procedure. The device is simple to use and is compatible with CT scanning, transrectal ultrasound, and the Mick applicator. Its design and key functional features are described here.

Brachytherapy↗

PubMed2002

A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.

Pseudogenes are open reading frames (ORFs) encoding dysfunctional proteins with high homology to known protein-coding genes. Although pseudogenes were reported to exist in the genomes of many eukaryotes and bacteria, no systematic search for pseudogenes in the Escherichia coli genome has been carried out. Genome comparisons of E. coli strains K-12 and O157 revealed that many protein-coding sequences have prematurely terminated orthologs encoding unstable proteins. To systematically screen for pseudogenes, we selected ORFs generated by premature termination of the orthologous protein-coding genes and subsequently excluded those possibly arising from sequence errors. Lastly we eliminated those with close homologs in this and other species, as these shortened ORFs may actually have functions. The process produced 95 and 101 pseudogene candidates in K-12 and O157, respectively. The assigned three-dimensional structures suggest that most of the encoded proteins cannot fold properly and thus are dysfunctional, indicating that they are probably pseudogenes. Therefore, the existence of a significant number of probable pseudogenes in E. coli is predicted, awaiting experimental verification. Most of them were found to be genes with paralogs or horizontally transferred genes or both. We suggest that pseudogenes constitute a small fraction of the genomes of free-living bacteria in general, reflecting the faster elimination than production of pseudogenes.

Amino Acid Sequence↗

PubMed2026

Rare genetic variant risks in patients with sepsis-associated acute respiratory distress syndrome.

BACKGROUND: Acute respiratory distress syndrome (ARDS) is a complex, heterogeneous, and deadly condition often resulting from pulmonary lesions due to sepsis, among other causes. There is a lack of targeted therapies to specifically treat the patients. Common genetic factors in the population (frequency > 1%) have been associated with ARDS susceptibility, but systematic genetic screens of the role of rare genetic variants are lacking. We used the network of known molecular interactions to identify ARDS risks from clusters of biologically related genes containing qualifying variants (QVs) with frequency < 1% likely affecting function. METHODS: We conducted whole-exome sequencing in sepsis patients from the GEN-SEP cohort (n = 822, of which 272 developed ARDS). A network-based heterogeneity clustering algorithm was used to discover significant gene clusters (p < 1 × 10–5). Gene-set enrichment analysis and logistic regression models aggregating QVs were used for cross-verification to confirm consistency and deepen understanding of the effect sizes of gene clusters. RESULTS: We identified 19 significant clusters (plowest = 3.29 × 10–10), each containing an average of 102 genes (11.6% mean similarity). QVs in nine gene clusters were associated with sepsis-associated ARDS (plowest = 1 × 10–5) but were not associated with 28-day survival. Clusters were enriched in several biological pathways, notably the Toll-like receptor cascades. CONCLUSIONS: These results support a marked genetic heterogeneity underlying ARDS susceptibility and the presence of rare risk variants involving multiple biological processes that are associated with sepsis outcomes. Particularly, they underscore the importance of rare variants in genes of the Toll-like receptor cascades in the risk for sepsis-associated ARDS.

Humans↗

PubMed2005

Fecal elastase: pancreatic status verification and influence on nutritional status in children with cystic fibrosis.

OBJECTIVES: To evaluate fecal elastase 1 (FE) levels in young children with cystic fibrosis and pancreatic insufficiency and to explore the relationship between FE and growth, nutrition, pulmonary status and fat absorption over a 24-month period. METHODS: FE, indicating pancreatic lipase activity, was assessed in children (6.0 to 8.9 years of age) with cystic fibrosis and pancreatic insufficiency. FE >15 microg/g stool was defined as residual pancreatic activity, suggesting some pancreatic function, and FE </=15 microg/g stool was defined as no pancreatic activity, suggesting pancreatic insufficiency. Seven-day weighed food records were collected and coefficient of fat absorption was calculated using dietary records and 72-hour stool collection. Height adjusted for mid-parental height, weight, body mass index, upper arm muscle area and upper arm fat area were measured and Z scores were calculated. Forced expiratory volume in 1 second was the measure of pulmonary function. RESULTS: Ten children (12%) had residual pancreatic activity (range, 17 to 667 microg/g stool) and 75 had no pancreatic activity. Children with no pancreatic activity had significantly lower coefficients of fat absorption than did those with residual pancreatic activity (81% +/- 14% versus 94% +/- 3%; P = 0.009) and significantly lower adjusted height Z score (-0.8 +/- 1.0 versus -0.1 +/- 1.3; P = 0.03). Children with residual pancreatic activity had significantly greater improvement in weight for age Z scores, upper arm muscle area Z scores, and upper arm fat area Z scores than children with no pancreatic activity (P </= 0.01). Children with no pancreatic activity were significantly (P = 0.007) more likely to have the DeltaF508/DeltaF508 genotype than were those with residual pancreatic activity (61% versus 11%). CONCLUSIONS: These data suggest that a substantial number (12% in this sample) of children with cystic fibrosis have a misclassified pancreatic status. Children with residual FE had greater fat absorption and improved growth and nutritional status over 24 months. FE assessment should be used to verify pancreatic status in patients with cystic fibrosis.

Anthropometry↗

PubMed2003

Live three-dimensional echocardiography: imaging principles and clinical application.

Live three-dimensional echocardiography (L3DE) is an important breakthrough in the field of medical ultrasound. It will provide a great potential tool for clinical diagnosis and treatment. In this article, the authors first review the bottlenecks in 3D cardiac imaging and the technical principles of L3DE that have been used to overcome some of these problems. We then discuss the scanning methods, clinical usefulness, and the future of L3DE, drawing on our experiences in examining 124 human patients and in conducting animal verification studies with a live 3D ultrasound system.

Echocardiography, Three-Dimensional↗

PubMed1998

Screen reconstructions: traumatic memory, conviction, and the problem of verification.

Just as formerly recalled screen memories may be remembered again in the course of psychoanalysis, so new screen phenomena can arise during the treatment process. This paper attempts to relate the process of reconstruction and the occurrence of a type of screening. It is proposed that, under certain circumstances, psychoanalysis can result in a mutually determined screen construction that both patient and analyst consider convincing and valid but which may, for the most part, actually be untrue as a result of the screen function. Screen memories arising during the reconstructive process resemble the déjà vu and déjà raconté situation in that the experience is felt with certainty to have actually occurred previously, although a degree of doubt about its having happened can consciously or unconsciously coincide. Factors contributing to the formation of screen constructions include regressive aspects of the analytic situation; superego elements and the experience of an injunction to remember; the wish to witness what took place in the past; direct or indirect suggestive influence by the analyst; a defensive identification with the analyst; and the analyst's theoretical orientation to reconstruction. Like a screen memory having some veridical content yet serving a masking function, a screen construction can have elements of truth. At the same time such constructions may function as a strong resistance of compromise against intense erotic, sadomasochistic, or narcissistic themes in the transference/counter-transference that were painful or conflictual in the past. If screen constructions are assumed to be historically real or valid, they may not be analyzed for their transferential screening role. A previously published case involving a presumably repressed memory of sexual molestation is considered from the perspective of the possible development of a screen reconstruction. Clinical and scientific aspects of seeking extra-analytic confirmation or falsification of reconstructions are discussed.

Adult↗

PubMed2006

Application of the quality index methodology for dosimetric verification of build-up effect beyond air-tissue interface in treatment planning system algorithms.

We have designed a simple benchmark test for the user of a treatment planning system to check the calculation algorithm's ability to model the build up effect beyond an air/tissue interface. The expected result is expressed as an inhomogeneity correction factor CF derived from measurements and from Monte Carlo calculations for a full range of photon beam qualities. The linear regression lines obtained from plotting CF as a function of beam quality index form the basis for a quantitative check of the algorithm performance.

Air↗

PubMed2005

Deletion of the SSK1 response regulator gene in Candida albicans contributes to enhanced killing by human polymorphonuclear neutrophils.

The isolation and partial functional characterization of the two-component response regulator SSK1 gene of Candida albicans was previously reported. Compared to wild-type (CAF2-1) and gene-reconstituted (SSK23) strains, the ssk1 null strain (SSK21) was avirulent in a murine model of hematogenously disseminated candidiasis and less able to adhere to human esophageal cells. More recent data indicate that SSK21 is sensitive to 4 to 8 mM H(2)O(2) in vitro than CAF2-1 and SSK23. Furthermore, microarray studies indicate that the regulation of two classes of genes, those encoding cell wall functions and stress adaptation, are altered in the ssk1 mutant. In the present study, the susceptibility of strains CAF2-1, SSK21, and SSK23 to killing by human polymorphonuclear neutrophils (PMNs) was assessed. Results are also described for a newly constructed ssk1 mutant (SSK24) in which the URA3 gene is integrated into its native locus. Our results indicate that killing of SSK21 and SSK24 was significantly greater than that of CAF2-1 and SSK23 (P < 0.01). In order to determine why Ssk1p at least partially protects the organism against the killing activity of human PMNs, we compared the signal transduction activity and the inflammatory response gene profiles of PMNs infected with either the wild type or the ssk1 mutant. Phosphorylation of the mitogen-activated protein kinases p42/44 and p38 from neutrophils infected with either CAF2-1 (wild type) or SSK21 (ssk1/ssk1) was similar, while expression and phosphorylation of the JNK mitogen-activated protein kinase was not observed following infection with either strain. On the other hand, we observed an upregulation of seven inflammatory response genes in PMNs infected with the SSK21 mutant only, while an increase in interleukin-10 expression was measured in PMNs infected with either strain. Downregulation of interleukin-2 was observed in PMNs infected with either strain. Verification of the transcriptional profiling was obtained by reverse transcription-PCR for three of the genes that were upregulated in neutrophils infected with the ssk1 mutant. Also, the sensitivity of strain SSK21 to human defensin-1, one of the nonoxidative, antimicrobial peptides of PMNs, was greater than that of CAF2-1, demonstrating that nonoxidative killing in PMNs may contribute to the increased susceptibility of the ssk1 mutant. Our results indicate that the Ssk1p response regulator protein may provide at least partial adaptive functions for the survival of C. albicans following its encounter with human neutrophils.

Candida albicans↗

PubMed2005

Compatibility of glass-guided recording microelectrodes in the brain stem of squirrel monkeys with high-resolution 3D MRI.

Knowledge of the precise position of recording microelectrodes within the brain of a non-human primate is essential for a reliable exploration of very small anatomic structures. This work demonstrates the compatibility of a newly developed glass-guided microelectrode design and microfeed equipment with high-resolution 3D magnetic resonance imaging (MRI). T1- and T2-weighted images allow for the non-invasive visualization of chronically implanted microelectrodes within the brain stem of squirrel monkeys in vivo. Neural extracellular multi-unit recordings proved the functionality of the microelectrode before and after the use of 3D MRI suggesting the preservation of normal brain tissue at the tip of the electrode. Because histology confirmed the absence of lesions attributable to MRI, the approach offers an interactive monitoring during the course of neuroethological experiments. Consequently, MRI may become an in vivo alternative to common histological post mortem verifications of electrode tracks and hence may avoid the early sacrificing of primates after only a small number of experiments.

Action Potentials↗

PubMed1994

Cesium abolishes the barium-induced pacemaker potential and current in guinea pig ventricular myocytes.

INTRODUCTION: The ability of cesium to block barium-induced diastolic depolarization ("Ba-DD") and pacemaker current was tested in isolated ventricular myocytes. Because Ba-DD is due to decreasing K+ conductance and there is no I(f) at the resting potential, this approach permits verification of whether Cs+ is a specific blocker of i(f) or if it instead also blocks a K+ pacemaker current. METHODS AND RESULTS: Guinea pig isolated ventricular myocytes were studied by a discontinuous, single electrode, voltage clamp method. During hyperpolarizing voltage clamp steps from -80 up to -140 mV in Tyrode's solution, the inward current increased as a function of voltage but did not change as a function of time (no I(f) or K+ depletion). Cesium (4 mM) reduced the current size during the hyperpolarizing steps but did not induce or unmask time-dependent currents. Barium (0.05 to 0.1 mM) induced diastolic depolarization, and, in its presence, depolarizing voltage clamp steps were followed by an outward tail current that reversed at -92.0 +/- 1.3 mV. Outward tail currents were larger at -50 mV than at the resting potential, and inward tail currents decayed more rapidly and to a larger extent during larger hyperpolarizing steps. In the presence of Ba2+, Cs+ (4 mM) had little effect on the steady-state current but markedly reduced or abolished undershoot, Ba-DD, and time-dependent tail currents at potentials both positive and negative to the resting potential. Cs+ had a smaller effect on the steady-state current-voltage (I-V) relation in the presence than in the absence of Ba2+, as part of the IK1 channels were already blocked by Ba2+ and the time-dependent changes induced by Ba2+ were not present. Both Ba2+ and Cs+ had little blocking effect on the steady-state current positive to the negative slope region of the I-V relation. CONCLUSION: In ventricular myocytes, Cs+ abolishes the Ba(2+)-induced pacemaker current by blocking the time-dependent change in K+ conductance, not by blocking I(f). Because Cs+ can also block a decaying K+ pacemaker current, the abolition of a pacemaker current by Cs+ in other cardiac tissues cannot be taken as unequivocal proof that the blocked current is I(f).

Animals↗

PubMed2002

[Orbital phlegmone caused by acute exacerbation of chronic fungal pansinusitis in a child].

INTRODUCTION: Invasive fungal rhinosinusitis is an aggressive, destructive process most commonly affecting immunocompromised hosts with mortality rate of approximately 60-80%. AIM OF STUDY: The authors present a child's recovery of orbital phlegmone due to acute exacerbation of chronic fungal pansinusitis. They call the attention to the possibility of ever more frequent fungal sinusitis in our country. METHODS: Retrospective case report of an 8 years old boy presented with photos. RESULTS: The recovery was promoted by supposing the chance of fungal origin in time. No orbital abscess was found by surgery despite of typical clinical appearance and MRI results. After beginning of antibacterial treatment and functional endoscopic sinus surgery (FESS) the even worsening clinical status of orbital phlegmone raised the possibility of fungal origin, which was verified by mycological examination. The antimycotic treatment, which had been started in time was followed by complete recovery. Due to scarring in the medial rectus muscle, diplopia was the only complication which needs further ophthalmological controls. CONCLUSIONS: Supposition and verification of chance of fungal origin is essential in cases of chronic inflammation of paranasal sinus and/or their complications for complex recovery.

Acute Disease↗

PubMed1989

[Comparative evaluation of the black foam film method for determining lung surfactant maturity in the newborn infant].

The present study evaluates a recently introduced method of black foam film (BFF) for determination of lung maturity, adapted for examination of nasopharyngeal aspirate (NFA) in the newborn and as well as to discover its diagnostic value by clinical verification and comparison with the method of total phospholipids (TPL) and with the ratio of lecithin/sphingomyelin (L/S). Comparing the results, obtained by the various methods, it was found that the capability of NFA of the newborn children to form BFF reflected the content of TPL and the ratio of L/S. The good correlation with the clinical state respectively with respiratory function of the examined children indicates the possibility that the method of BFF could be used for postnatal evaluation of lung maturity.

Evaluation Studies as Topic↗

PubMed2005

Overt naming in aphasia studied with a functional MRI hemodynamic delay design.

The purpose of this study was to develop a functional MRI method to examine overt speech in stroke patients with aphasia. An fMRI block design for overt picture naming was utilized which took advantage of the hemodynamic response delay where increased blood flow remains for 4-8 s after the task [(Friston, K.J., Jezzard, P., Turner, R., 1994. Analysis of functional MRI time-series. Hum. Brain Mapp. 1, 153-171)]. This allowed task-related information to be obtained after the task, minimizing motion artifact from overt speech (Eden, G.F., Joseph, J., Brown, H.E., Brown, C.P., Zeffiro, T.A., 1999. Utilizing hemodynamic delay and dispersion to detect fMRI signal change without auditory interference: the behavior interleaved gradients technique. Magn. Reson. Med. 41, 13-20; Birn, RM., Bandettini, P.A., Cox, R.W., Shaker, R., 1999. Event-related fMRI of tasks involving brief motion. Hum. Brain Mapp. 7, 106-114; Birn, R.M., Cox, R.W., Bandettini, P.A., 2004. Experimental designs and processing strategies for fMRI studies involving overt verbal responses. NeuroImage 23, 1046-1058). Five chronic aphasia patients participated (4 mild-moderate and 1 severe nonfluent/global). The four mild-moderate patients who correctly named 88-100% of the pictures during fMRI, had a greater number of suprathreshold voxels in L supplementary motor area (SMA) than R SMA (P < 0.07). Three of these four mild-moderate patients showed activation in R BA 45 and/or 44; along with L temporal and/or parietal regions. The severe patient, who named no pictures, activated almost twice as many voxels in R SMA than L SMA. He also showed activation in R BA 44, but had remarkably extensive L and R temporal activation. His poor naming and widespread temporal activation may reflect poor modulation of the bi-hemispheric neural network for naming. Results indicate that this fMRI block design utilizing hemodynamic response delay can be used to study overt naming in aphasia patients, including those with mild-moderate or severe aphasia. This method permitted verification that the patients were cooperating with the task during fMRI. It has application for future fMRI studies of overt speech in aphasia.

Aged↗

PubMed2000

An orthogonal moment-based method for automatic verification of radiation field shape.

The purpose of this paper is to develop a new method for automated on-line verification of the treatment field shape during radiotherapy. The treatment field boundary is extracted from the digital portal image and is then approximated by a polygon. The proposed procedure used one of the approved field shapes as the reference boundary for automated comparison with subsequent portal field boundaries. The orthogonal moment-based method was applied to align treatment field boundaries that include the translational shifts, scaling factor and rotation angle. Firstly, the moments of order up to one were used to adjust the magnification and translation of the test field boundary related to the reference one; this step created a common coordinate system for the two images. Then a quadratic least-square objective function based on the orthogonal moments (e.g. Legendre moments) of the two field shapes was employed to perform rotational correction. Since moment computation by a straightforward method required a large number of multiplication and addition operations, a fast method for computing Legendre moments was also developed to decrease the calculation time. Application of the method to some simulated cases showed that our alignment procedure has an accuracy of 0.5 mm in detecting translational shift, 0.004 in detecting magnification and less than 0.3 degrees in detecting rotation angle between the test shape and the reference shape. The alignment procedure using the proposed method can be done within 2 s on a Pentium II personal computer. Therefore, our method is potentially useful for automated real-time treatment field shape verification.

Algorithms↗

PubMed1989

Behavioural responses to cerebellar stimulation in cerebral palsy.

Stereotactic placement of stimulating electrodes (TESLA) into deep regions of the cerebellum (Fischer instruments) was analyzed in respect to its organization into sagittaly oriented zones. This was done after imaging of the trajectory and target area and verification of the position of electrodes by CT (Siemens). A correlation was observed between the position of the stimulating electrode from the midline laterally and localization of induced responses on the body--from bilateral to ipsilateral. The combination of deep cerebellar stimulation and destructive method in the supratentorial region could be the optimal approach to relieve spasticity and to improve motor function in some cases of cerebral palsy.

Brain Mapping↗

PubMed2006

Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair.

The human xeroderma pigmentosum group B (XPB) helicase is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. Here, we determined crystal structures of an Archaeoglobus fulgidus XPB homolog (AfXPB) that characterize two RecA-like XPB helicase domains and discover a DNA damage recognition domain (DRD), a unique RED motif, a flexible thumb motif (ThM), and implied conformational changes within a conserved functional core. RED motif mutations dramatically reduce helicase activity, and the DRD and ThM, which flank the RED motif, appear structurally as well as functionally analogous to the MutS mismatch recognition and DNA polymerase thumb domains. Substrate specificity is altered by DNA damage, such that AfXPB unwinds dsDNA with 3' extensions, but not blunt-ended dsDNA, unless it contains a lesion, as shown for CPD or (6-4) photoproducts. Together, these results provide an unexpected mechanism of DNA unwinding with implications for XPB damage verification in nucleotide excision repair.

Amino Acid Motifs↗