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PubMed2005

A theoretical study for the reaction of vinyl cyanide C2H3CN(X1A') with the ground state carbon atom C(3P) in cold molecular clouds.

The reaction of the ground state atomic carbon, C(3P), with simple unsaturated nitrile, C2H3CN(X1A' (vinyl cyanide), is investigated theoretically to explore the probable routes for the formation of carbon-nitrogen-bearing species in extraterrestrial environments particularly of ultralow temperature. Five collision complexes without entrance barrier as a result of the carbon atom addition to the pi systems of C2H3CN are characterized. The B3YLP/6-311G(d,p) level of theory is utilized in obtaining the optimized geometries, harmonic frequencies, and energies of the intermediates, transition states, and products along the isomerization and dissociation pathways of each collision complex. Subsequently, with the facilitation of computed RRKM rate constants at collision energy of 0-10 kcal/mol, the most probable paths for each collision complexes are determined, of which the CCSD(T)/6-311G(d,p) energies are calculated. The major products predicted are exclusively due to the hydrogen atom dissociations, while the products of H2, CN, and CH2 decompositions are found negligible. Among many possible H-elimination products, cyano propargyl (p4) and 3-cyano propargyl (p5) are the most probable, in which p5 can be formed via two intermediates, cyano allene (i8) and cyano vinylmethylene (i6), while p4 is yielded from i8. The study suggests this class of reaction is an important route to the synthesis of unsaturated nitriles at the temperature as low as 10 K, and the results are valuable for future chemical models of interstellar clouds.

Journal Article↗
PubMed1996

Cerebral venous sinus thrombosis associated with systemic multiple hemangiomas manifesting as chronic subdural hematoma--case report.

A 35-year-old male was admitted with headache, nausea, and vomiting persisting for 2 days. Computed tomography (CT) revealed a left chronic subdural hematoma. Cerebral angiography demonstrated cerebral venous sinus thrombosis (CVST). He had presented with a subcutaneous mass involving the neck at age 2 years, which was shown to be a cavernous angioma, and thereafter shown signs of consumptive coagulopathy with systemic multiple hemangiomas. Burr hole aspiration of the hematoma was performed. Seventy-two-hours later, he developed clouding of consciousness and right hemiparesis. CT revealed a fresh hematoma in the operated subdural cavity and hemorrhagic diathesis manifested. A frontotemporoparietal large craniotomy was performed to remove the hematoma. Extensive electrocauterization was required. He had a satisfactory postoperative course. Collateral venous pathways, resulting from the CVST due to systemic multiple hemangiomas, may have caused hemodynamic stress in the bridging veins which subsequently induced chronic subdural hematoma.

Adult↗
PubMed2001

Evaluation of the models available for the prediction of pressure drop in venturi scrubbers.

The major running cost derived from the operation of venturi scrubbers is pressure drop. In the present study, the predictions of different models are compared to experimental data from venturi scrubbers of different sizes (throat diameter from 1.9 to 16cm), geometries, operating variables and liquid injection arrangements. As a result, it is concluded that most of the models must be used with caution. Much attention must be paid to the validity of the assumptions employed in the mathematical models. The equations proposed by Calvert [Scrubbing, Air Pollution, 3rd Edition, Vol. IV, Academic Press, New York, 1982], Yung et al. [JAPCA 27 (1977) 348] or Hesketh [Atomization and cloud behaviour in wet scrubbers, in: Proceedings of the US-USSR Symposium Control Fine Particulate Emissions 1974, San Francisco, 15-18 January 1974] produce good results only in very specific situations. The model proposed by Boll [Ind. Eng. Chem. Fundam. 12 (1973) 40] is simple, easy to compute and agrees reasonably well with the experimental data. Unfortunately, it cannot predict the effect of different liquid injection arrangements. The model by Azzopardi and coworkers [Filtr. Sep. 21 (1984) 196; Trans. IchemE. 69B (1991) 237; Chem Eng. J. 67 (1997) 9] was the only one to give good predictions for all the range of variables studied. On the other hand, this model is not simple and requires from the engineer an additional effort in terms of computation. In order to apply this model to the rectangular geometry, the concept of hydraulic equivalent diameter was used.

Aerosols↗
PubMed2004

Advances in neuroimaging for HIV-1 associated neurological dysfunction: clues to the diagnosis, pathogenesis and therapeutic monitoring.

Persons with advanced human immunodeficiency virus type one (HIV-1) infection seek medical advice for a wide range of neurological disorders including, but not limited to, peripheral neuropathy, toxoplasmosis, cryptococcal meningitis, cytomegalovirus retinitis progressive multifocal leukoencephalopathy, lymphoma and dementia. The diagnosis of HIV-1-associated dementia (HAD) induced as a direct consequence of HIV infection of the brain comes commonly by exclusion. Diagnostic decisions can often be clouded by concomitant depression, motor impairments, and lethargy that follow debilitating immune suppression and weight loss. Indeed, cognitive, motor and behavior abnormalities underlie a variety of neurological dysfunctions associated with advanced HIV-1 infection. Thus, even combinations of clinical, laboratory and neuroimaging tests [for example, magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET)] often fail to provide conclusive diagnostic information. Nonetheless, the recent development of quantitative MR spectroscopic imaging has improved diagnostic possibilities for HAD. We are pleased to discuss these developments as well as taking a forward look into what will soon be made available to improve neuroimaging diagnostic precision. New MR and SPECT testing are being developed in our laboratories and elsewhere both for animal model systems and in humans with HIV-1 disease. Such tests can facilitate dynamic measures of HIV-1 neuropathogenesis providing information for disease events that even 2 years ago were unattainable.

AIDS Dementia Complex↗
PubMed2006

Stratus not altocumulus: a new view of the yeast protein interaction network.

Systems biology approaches can reveal intermediary levels of organization between genotype and phenotype that often underlie biological phenomena such as polygenic effects and protein dispensability. An important conceptualization is the module, which is loosely defined as a cohort of proteins that perform a dedicated cellular task. Based on a computational analysis of limited interaction datasets in the budding yeast Saccharomyces cerevisiae, it has been suggested that the global protein interaction network is segregated such that highly connected proteins, called hubs, tend not to link to each other. Moreover, it has been suggested that hubs fall into two distinct classes: "party" hubs are co-expressed and co-localized with their partners, whereas "date" hubs interact with incoherently expressed and diversely localized partners, and thereby cohere disparate parts of the global network. This structure may be compared with altocumulus clouds, i.e., cotton ball-like structures sparsely connected by thin wisps. However, this organization might reflect a small and/or biased sample set of interactions. In a multi-validated high-confidence (HC) interaction network, assembled from all extant S. cerevisiae interaction data, including recently available proteome-wide interaction data and a large set of reliable literature-derived interactions, we find that hub-hub interactions are not suppressed. In fact, the number of interactions a hub has with other hubs is a good predictor of whether a hub protein is essential or not. We find that date hubs are neither required for network tolerance to node deletion, nor do date hubs have distinct biological attributes compared to other hubs. Date and party hubs do not, for example, evolve at different rates. Our analysis suggests that the organization of global protein interaction network is highly interconnected and hence interdependent, more like the continuous dense aggregations of stratus clouds than the segregated configuration of altocumulus clouds. If the network is configured in a stratus format, cross-talk between proteins is potentially a major source of noise. In turn, control of the activity of the most highly connected proteins may be vital. Indeed, we find that a fluctuation in steady-state levels of the most connected proteins is minimized.

Computational Biology↗
PubMed2007

Solutions to the Gaussian cloud approximation for gamma absorbed dose.

Analytical solutions of the dose rate integral for the Gaussian cloud approximation to the Gaussian plume were developed. A solution for the I1 integral for a ground-level source and for the I2 integral for an elevated source were given in terms of special functions. The I2 solution was also extended for the Berger buildup factor. These enable rapid computation of I1 and I2 to estimate the dose rate.

Air Pollutants, Radioactive↗
PubMed2006

Spin correlations and finite-size effects in the one-dimensional kondo box.

We analyze the Kondo effect of a magnetic impurity attached to an ultrasmall metallic wire using the density matrix renormalization group. The spatial spin correlation function and the impurity spectral density are computed for system sizes of up to L=511 sites, covering the crossover from L l{K}, with l{K} the spin screening length. We establish a proportionality between the weight of the Kondo resonance and l{K} as a function of L. This suggests a spectroscopic way of detecting the Kondo cloud.

Journal Article↗
PubMed2001

Laser scanning of patient outlines for three-dimensional radiotherapy treatment planning.

In the planning of radiation treatments it is important to have a knowledge of the patient outline in order to correctly calculate the dose distribution that can be expected within the patient. This information is routinely obtained using x-ray computed tomography (CT). Although the CT data set is the ultimate data set, it can be impractical for economic and physical reasons. These impracticalities have been overcome using a commercial three dimensional (3D) laser scanning system. The system scans a laser line across the surface of the patient while a CCD camera views the patient from an offset angle. From a knowledge of the spatial orientation of the camera and the laser source, the system is able to detect the patient's surface and generate an equivalent 3D point cloud. Manipulation of 3D data sets allows the appropriate outlines of the patient to be obtained, that can then be used with the radiotherapy planning system. This has enabled the evaluation of 3D dose distributions for patients, and hence will allow the development of techniques for improving the uniformity of dose in breast treatments. The technique has no radiation overhead associated with it, is quick and is relatively cheap.

Breast↗
PubMed2006

[3D-data acquisition of partially edentulous cast using grating projection method].

OBJECTIVE: A method for 3D-data acquisition of partially edentulous cast was introduced to lay the foundation for reconstructing 3D digital model of a partially edentulous cast and studying computer aided design (CAD) to a removable partial denture framework. METHODS: Using projection system controlled by a computer, four frames of sinusoidal fringe pattern at pi/2 intervals were projected onto the surface of partially edentulous cast consecutively within 0.4 second. Deformed fringe patterns modulated by the surface height of the cast were recorded by a digital camera. The phase value with the height information was demodulated with phase-shifting method. The transition from the unwrapped phase to the height of the points on the cast was performed with triangulation method. The multiview 3D data was integrated automatically to obtain the complete 3D profile data and the 3D digital model of the partially edentulous cast was reconstructed. RESULTS: Dense and complete points-cloud data was achieved without scanning blind zone basically. The anatomic structure of reconstructed 3D digital model was sharp and clear. CONCLUSION: As an alternative for acquiring 3D data of partially edentulous cast, this method presented here with high precision and high speed meets the need for the subsequent 3D design to removable partial denture framework.

Computer-Aided Design↗
PubMed2005

The low energy tautomers and conformers of the dipeptides HisGly and GlyHis and of their sodium ion complexes in the gas phase.

The low-lying conformers of the dipeptides HisGly and GlyHis, and of their sodium cation complexes, have been studied with a combination of Monte Carlo search with the Amber force field and local geometry optimization at the ab initio HF/6-31G(d) level, completed with MP2(full)/6-311+G(2d,2p) energetics at the HF/6-31G(d) geometries. For each dipeptide, both the N(delta)-H and N(epsilon)-H tautomers of the imidazole side chain of His were considered. For each of the four isomeric dipeptides, 20-30 conformers were fully characterized at the ab initio level. All low energy structures are found to involve H-bonding at the N(delta) position of imidazole, either as a N-H donor or a N acceptor, depending upon the tautomer. In three out of the four species, the most stable conformer involves a C-terminus carboxylic acid in its less favorable trans conformation, in order to maximize intramolecular H bonding. It turns out that the lowest energy tautomer of HisGly is N(epsilon)-H, while that of GlyHis is N(delta)-H. This result argues in favor of the diversity of His tautomeric states in peptides and proteins. The sodium cation complexes of both GlyHis and HisGly have been studied as well, again considering both tautomers in each case. In three out of the four species, the most stable structure involves chelation of sodium by the two carbonyl oxygens and the imidazole ring. On the contrary, the sodium complex of the N(delta)-H tautomer of HisGly favors chelation to the peptidic carbonyl oxygen, the imidazole ring and the amino terminus. In the N(epsilon)-H tautomers of both peptides, the most favorable binding site of imidazole is the N(delta) nitrogen, while in the N(delta)-H tautomers, it is the pi cloud which provides side chain interaction. As a result, both GlyHisNa+ and HisGlyNa+ favor the N(epsilon)-H tautomer of His, in contrast to what was found for the free peptides.

Computer Simulation↗
PubMed1994

T/A-analysis with or without measuring force: problems in the evaluation of normal limits.

Turn/amplitude-analysis (TAA) has been applied to interference patterns of the right m. biceps brachii and the right m. rectus femoris of 33 healthy women aged 19 to 53 years. Interference patterns were recorded at 20, 40 and 60% +/- 10% of both muscles maximum force. The dependency of the turn/amplitude-parameters (T/A-parameters) on age, muscle and force is discussed. Normal limits for individual means of the T/A-parameters were calculated in form of the +/- 2 SD. Normal limits for single values were calculated in form of clouds. Both methods were applied to the values of each force level (20, 40 and 60%) and of all force levels together (10-70%). Clouds of the present study were clearly different from those of Stålberg. Evaluating individual means rates of false positive results were higher compared to those of single values. Rates of false positive results for single values and individual means of the parameters T/S and A/T were lower at the 20% force level than at the higher force levels and without measuring force. For the application of the TAA we advise every electrophysiological laboratory 1) to evaluate single values instead of individual means, 2) to use clouds instead of the +/- 2 SD as normal limits, 3) to measure force until a modified cloud-method will be applicable and 4) to elaborate its own normal limits.

Adult↗
PubMed1989

[Antemortem diagnosis of Marchiafava-Bignami disease].

Marchiafava-Bignami disease (M-B disease) is a peculiar disease, observed in hardened drinkers and resulting in demyelinization and necrosis of the corpus callosum. The clinical symptoms are diverse, and it is difficult to diagnose accurately while the patient is alive. Almost all reports in the past have been based on necropsy. Only three cases of M-B disease have been reported in Japan so far, none of which was based on a diagnosis while the patient was alive. We have been able to perform diagnosis of M-B disease while the patients were still alive by means of X-ray computed tomography (CT) and magnetic resonance imaging (MRI), and to study the clinical symptoms from the acute stage. In addition to the study on our own patients, we also conducted a neurosymptomatic study on the clinical symptoms of 6 cases, for which details of the symptomatology have been described-out of about 150 cases reported in the past. In the acute stage of M-B disease, we observed psychic symptoms, such as clouding of consciousness, mnemonic disorders and disorders and disorientation, or various frontal lobe symptoms, such as change in personality, raptus nervorum, dysphemia, pyramidal signs and astasia-abasia. These are non-specific symptoms and it is necessary to differentiate from encephalitis and other encephalopathy. In the chronic stage, dysphemia becomes sustained and, in addition, symptoms of transection of the corpus callosum are noted among the disorders of higher cerebral functions. If M-B disease is suggested from clinical symptoms, it is advisable to confirm the lesions in the corpus callosum by X-ray CT and MRI.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2005

[Giant seminoma in abdominal retention of the testis manifested with unilateral leg pain: a case report].

A 26-year-old man was admitted to the department of surgery of our hospital with a complaint of intermittent left leg pain for the past two weeks. Ultrasonography revealed reduced blood flow to the tibial artery, which suggested a vascular disease like arteriosclerosis obliterans. Enhanced computed tomography (CT) revealed a huge abdominal tumor and a 3-dimensional CT scan showed a feeding artery from the left renal artery to the huge tumor. Findings of routine blood and urine examinations were elevated levels of lactate dehydrogenase, alkaline phosphatase, and C-reactive protein. Surgical exploration revealed a giant tumor with clouded ascites in the abdominal cavity containing class V cells revealed by cytological examination. The tumor was easily resected. Its vascular pedicle was thick and hypertrophied. Thus, it could be traced to the origin of left gonadal artery. At this time, the surgeon incidentally noticed the absence of left testis in the patient's scrotum. The resected specimen was 25 x 18 x 12 cm in size, and it weighed 3000 gm. The histological finding was pure seminoma invaded to peritoneum. His leg pain was relieved after the tumor resection.

Adult↗
PubMed2004

High-resolution laser surface scanning for patient registration in cranial computer-assisted surgery.

OBJECTIVE: Markerless patient registration is a new procedure that may reduce logistical efforts and possibly also the radiation load on the patients prior to a computer-assisted intervention. Congruent surfaces, such as bone surfaces or skin surfaces, represented in a data set and in the surgical site, can be overlapped using surface-matching. Previous studies describing this kind of markerless registration, however, show inaccuracies of up to 10 mm during computer-assisted navigation. Furthermore, these systems use less than 1000 surface points of the soft tissue surface in order to establish a correlation between the patient and the data set. Previous papers did not answer the question whether it is this scanning resolution that induces these inaccuracies in registration or rather intraoperative skin deformations. STUDY DESIGN: In the present study therefore a new navigation system (SSN++) was used which is able to register up to 180,000 surface points of the surgical site. SSN++ is an infrared navigation system enlarged by a Minolta VI 900 3D volume digitizer. Three different kinds of laser scan-resolution were used for data correlation. An additional congruence analysis was performed in order to assess the geometry of the matched skin surfaces. 22 patients suffering from different cranial diseases (tumors, bony malformations, foreign bodies) were prepared for a computer-assisted intervention. Intraoral titanium-markers, rigidly fixed on the patients by a maxillary splint, were placed as targets while the CT data sets were made. These targets were - after markerless laser scan registration of the patients - supposed to serve for validating the new high-resolution navigation system SSN++. RESULTS: The accuracy of markerless laser scan registration depends on the intraoperative laser scan's resolution. A high accuracy of the data correlation can be achieved if the number of the laser scan cloud points is about the same as the number of voxels of the corresponding surface on the CT data set. A reduction of the laser scan cloud points to less than 10 % compared to the number of voxels of the CT surface, however, leads to a significant loss of accuracy after markerless patient registration. CONCLUSION: The markerless laser scan registration of the surgical site may achieve the same accuracy as a patient registration made by rigidly fixed titanium screws (mean accuracy: 1.2 mm) as long as a high-resolution laser scan is being used.

Brain Diseases↗
PubMed2003

Shallow layer simulation of heavy gas released on a slope in a calm ambient. Part II. Instantaneous releases.

This paper assesses the value of shallow layer modelling for instantaneous releases of heavy gas over a slope using the established computer model TWODEE [R.K.S. Hankin, Heavy gas dispersion over complex terrain, Ph.D. thesis, Cambridge University, 1997; J. Hazard. Mater. 66 (1999) 211; J. Hazard. Mater. 66 (1999) 227; J. Hazard. Mater. 66 (1999) 239] and the experimental results of Schatzmann et al. [M. Schatzmann, K. Marotzke, J. Donat, Research on continuous and instantaneous heavy gas clouds, Contribution of sub-project EV 4T-0021-D to the final report of the joint CEC project, Technical report, Meteorological Institute, University of Hamburg, February 1991]. This is the second of a two-part paper; part I considered continuous releases using the same model, using the same entrainment parameters. Schatzmann et al. carried out instantaneous releases of heavy gas over three slopes; each experiment was repeated five times under nominally identical conditions. The goodness-of-fit measures (GFMs) of Hanna et al. [Atmos. Environ. 27A (15) (1993) 2265] are generalized to account for the multiple releases carried out by Schatzmann et al. Using these statistical GFMs, predicted peak concentrations are generally correct to within a factor of two; and cloud arrival times are generally late.

Air Pollutants↗
PubMed2026

Managing workflow executions with WESkit.

SUMMARY: In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. It addresses the complexities involved in managing numerous executions with varying parameters across diverse research projects. Supporting both Snakemake and Nextflow, the system enables consistent automation and centralized monitoring, which benefits research groups aiming for long-term reproducibility and scalable collaboration. Its suitability for larger teams and service units is further enhanced by seamless integration into cloud environments, contributing to the GA4GH cloud framework. AVAILABILITY AND IMPLEMENTATION: The software WESkit is available under MIT license at the GitLab repository (https://gitlab.com/one-touch-pipeline/weskit). The WESkit main repository is archived at Software Heritage (https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/one-touch-pipeline/weskit/api.git) and can be found using "one-touch-pipeline/weskit" term in the search section.

Workflow↗
PubMed2000

Construction and testing of a computer-based intraoral laser scanner for determining tooth positions.

An optical set-up for intraoral data acquisition based on the principle of laser triangulation was developed. The system consists of a pig-tailed laser with line generating optics, a stepping motor driven positioning stage, a commercial CCD (charge coupled device) camera system with frame grabber interface, a control personal computer and a mirror system compensating for the fact that there is no possibility of watching an object directly in the mouth under a certain angle except from a facial position during intraoral scanning. Due to the size of the prototype measurements were still restricted to plaster casts. In order to evaluate its accuracy, the measurements were compared with those taken with a commercial laser scanner and a coordinate measurement table. The accuracy of the prototype scanner was determined to be DeltaXYZ=0.04 mm using gauge blocks of given dimensions and proved to range between the commercial laser scanner and the coordinate measurement table (i.e., it was slightly better than that of the commercial scanner). Applications in orthodontics were demonstrated by scanning plaster casts and measuring distances on reconstructed surfaces. The measured distances showed a maximum deviation of about +/-0.2 mm compared with the data of the coordinate measurement table, which served as a reference. In addition, reconstruction of three-dimensional tooth movements was performed on the scan data. The translational and rotational parameters gained from the superimposition of scanned point clouds and describing tooth movement were also in good accordance with the reference. The achieved accuracy proved to be sufficient for further development which should include a reduction in size and the use of more precise device components.

Dental Occlusion↗
PubMed2005

A computational study of [2.2]cyclophanes.

A computational study of isomeric [2.2]cyclophanes, namely [2.2]paracyclophane 1, [2.2]metacyclophane 2, and [2.2]metaparacyclophane 3, has been carried out. For 1, geometry optimizations performed by various methods at different basis sets showed that MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison to the X-ray data. Compound 1 has D(2) symmetry with distorted bridges. A conformational search was performed for [2.2]cyclophanes 2 and 3. Each cyclophane exists in two conformations which have different energies in the case of 3 but are degenerate in the case of 2. Relative energies and strain energies at the bridges follow the same order, indicating that the relief of bridge tension and repulsion between pi clouds are determining factors for the stability of [2.2]cyclophanes. Through a decomposition of strain energy, it can be concluded that both the rings or the bridges can absorb strain, but it depends on the conformer of butane that is considered in the calculation of SE(br). Changes in aromaticity of these compounds were evaluated by NICS and HOMA and were compared with benzene and xylenes dimers as models. Despite distortions from planarity and shortening and lengthening of the C-C bonds relative to the mean, the phenyl rings are aromatic. NICS suggests a concentration of electronic density between the rings as a result of bridging process. Computed MK, NPA, and GAPT charges were compared for the isomeric cyclophanes. The GIAO chemical shifts were calculated and indicate that 1 has a larger diamagnetic anisotropy than the other isomers.

Journal Article↗