Phan Rim - Academia.edu (original) (raw)

Papers by Phan Rim

Pediatric Nephrology, 2003

Autosomal recessive polycystic kidney disease (ARPKD) is a relatively common form of pediatric po... more Autosomal recessive polycystic kidney disease (ARPKD) is a relatively common form of pediatric polycystic kidney disease with an incidence of 1:20,000 live births. Previous reports, primarily from populations of European origin, indicate that the clinical presentation and disease course are quite variable. Using a retrospective study design, we sought to determine whether the clinical course and outcome of our multi-ethnic patient cohort differs from the published literature. A 10-year (1990–2000) retrospective study was conducted in which we reviewed the clinical, histopathological, and imaging records of our 31 ARPKD patients. Patients were diagnosed between 0 and 14 years of age, with 17 (55%) presenting within the 1st month of life. The mean follow-up was 67 months and age at last follow-up ranged from 0.5 to 16 years. Of the 17 patients diagnosed as neonates, 11 (65%) had respiratory insufficiency complicated by pneumothoraces. Two died shortly after birth and 2 died within the 1st year of life due to respiratory failure. Among the 13 neonatal survivors, 7 (54%) developed progressive renal insufficiency, whereas 6 of 14 (43%) of those children who presented beyond 1 month of age developed renal insufficiency. Hypertension was present in 55% of our patients, with nearly all neonatal survivors requiring antihypertensive management. Evidence of portal hypertension was found in 10 (37%) of the 27 patients who survived the 1st year of life. In our multi-ethnic ARPKD cohort, the 1-year survival rate (87%) and the clinical variability are comparable to those previously reported. With the recent identification of the PKHD1 gene, characterization of disease-causing mutations should provide new insights into the molecular basis for this phenotypic variability.

Rheologica Acta, 1999

Edge fracture is an instability of cone-plate and parallel plate flows of viscoelastic liquids an... more Edge fracture is an instability of cone-plate and parallel plate flows of viscoelastic liquids and suspensions, characterised by the formation of a `crack' or indentation at a critical shear rate on the free surface of the liquid. A study is undertaken of the theoretical, experimental and computational aspects of edge fracture. The Tanner-Keentok theory of edge fracture in second-order liquids is re-examined and is approximately extended to cover the Criminale-Ericksen-Filbey (CEF) model. The second-order theory shows that the stress distribution on the semi-circular crack is not constant, requiring an average to be taken of the stress; this affects the proportionality constant, K in the edge fracture equation −N 2c = KΓ/a, where N 2c is the critical second normal stress difference, Γ is the surface tension coefficient and a is the fracture diameter. When the minimum stress is used, K = 2/3 as found by Tanner and Keentok (1983). Consideration is given to the sources of experimental error, including secondary flow and slip (wall effect). The effect of inertia on edge fracture is derived. A video camera was used to record the inception and development of edge fracture in four viscoelastic liquids and two suspensions. The recorded image was then measured to obtain the fracture diameter. The edge fracture phenomenon was examined to find its dependence on the physical dimensions of the flow (i.e. parallel plate gap or cone angle), on the surface tension coefficient, on the critical shear rate and on the critical second normal stress difference. The critical second normal stress difference was found to depend on the surface tension coefficient and the fracture diameter, as shown by the theory of Tanner and Keentok (1983); however, the experimental data were best fitted by the equation −N 2c = 1.095Γ/a. It was found that edge fracture in viscoelastic liquids depends on the Reynolds number, which is in good agreement with the inertial theory of edge fracture. Edge fracture in lubricating grease and toothpaste is broadly consistent with the CEF model of edge fracture. A finite volume method program was used to simulate the flow of a viscoelastic liquid, obeying the modified Phan-Thien-Tanner model, to obtain the velocity and stress distribution in parallel plate flow in three dimensions. Stress concentrations of the second normal stress difference (N 2) were found in the plane of the crack; the velocity distribution shows a secondary flow tending to aid crack formation if N 2 is negative, and a secondary flow tending to suppress crack formation if N 2 is positive.

Geosciences Journal, 2009

To constrain the timing of collisional event in the Indochina block, SHRIMP U-Pb dating and REE a... more To constrain the timing of collisional event in the Indochina block, SHRIMP U-Pb dating and REE analyses of zircon were carried out for two paragneiss samples of the Kham Duc Complex, central Vietnam. Both samples contain kyanite, staurolite, and zoisite as relics from an early metamorphic stage (M1), and biotite and sillimanite as major minerals constituting the foliation formed during the late metamorphic stage (M2). The change in mineral assemblages indicates a clockwise P-T path composed of a high- or medium-P + low-T stage (M1) and a subsequent low- P + high-T stage (M2). The U-Pb concordia ages of zircon rims are 447 ± 6 Ma and 452 ± 6 Ma for the two samples, respectively. These results are distinctly different from the available Ar-Ar mineral ages of 254–225 Ma. Following the clockwise P-T path and phase equilibrium analyses of the Complex, we suggest that the zircon rims were formed near peak temperatures during the decompression. The ∼450 Ma zircon rim thus gives the minimum age constraint for a possible crustal thickening event during Early Paleozoic, whereas the reported Permo-Triassic Ar-Ar ages would result from an Indosinian overprint. This Early Paleozoic event is most likely related to a collisional orogeny between the Indochina and South China blocks. Late Neoproterozoic to Neoarchean ages are recorded from detrital zircon cores of the Kham Duc Complex, the Kontum Massif and Truong Son Belt, suggesting that their protoliths might have derived from sediments at the Gondwana margin.

Rheologica Acta, 2007

Flow instability in three entangled polymer systems including a 10 wt% 1,4-polybutadiene (PBD) so... more Flow instability in three entangled polymer systems including a 10 wt% 1,4-polybutadiene (PBD) solution, an 11.4 wt% polyisobutylene (PIB) solution, and a long chain branched polyethylene melt (LD 146) was investigated in both stress-controlled and rate-controlled experiments in the cone–plate geometry. It was found that flow instability occurred for experiments in both rate- and stress-controlled modes. The effects of cone angle or rim gap and shearing time on flow instability were studied. The smaller cone angle and shorter shearing time delay (in terms of stress or shear rate) the occurrence of severe instability and mass loss of the PBD solution but not for the PIB. Our data are consistent with the dramatic shear rate jump for the flow curve constructed from the stress-controlled experiments being associated with mass loss after the severe instabilities. We also find that the Cox–Merz representation gives a powerful tool for investigation of flow instability. Finally, another interesting result in this work is that it seems that the stress overshoot can be related to the onset of flow instability in the present system.

Journal of Electrostatics, 1997

Surface waves on a thin oil film placed on top of a ground-supported dielectric sheet has recentl... more Surface waves on a thin oil film placed on top of a ground-supported dielectric sheet has recently been observed to exist when the oil film has been precharged adequately and when a sharp grounded electrode is suddenly introduced into the vicinity of the oil layer .

Expert Systems With Applications

As new high-throughput technologies have created an explosion of biomedical literature, there ari... more As new high-throughput technologies have created an explosion of biomedical literature, there arises a pressing need for automatic information extraction from the literature bank. To this end, biomedical named entity recognition (NER) from natural language text is indispensable. Current NER approaches include: dictionary based, rule based, or machine learning based. Since there is no consolidated nomenclature for most biomedical NEs, any NER system relying on limited dictionaries or rules does not seem to perform satisfactorily. In this paper, we consider a machine learning model, CRF, for the construction of our NER framework. CRF is a well-known model for solving other sequence tagging problems. In our framework, we do our best to utilize available resources including dictionaries, web corpora, and lexical analyzers, and represent them as linguistic features in the CRF model. In the experiment on the JNLPBA 2004 data, with minimal postprocessing, our system achieves an F-score of 70.2%, which is better than most state-of-the-art systems. On the GENIA 3.02 corpus, our system achieves an F-score of 78.4% for protein names, which is 2.8% higher than the next-best system. In addition, we also examine the usefulness of each feature in our CRF model. Our experience could be valuable to other researchers working on machine learning based NER.

The most important clinical indications for magnetic resonance imaging (MRI) are assessment of ca... more The most important clinical indications for magnetic resonance imaging (MRI) are assessment of cartilage in osteoarthritis (OA), chronic or acute osteochondral injury including sports injuries, osteochondritis dissecans, chondromalacia patellae, and inflammatory arthropathies (in particular before invasive therapy). In addition dedicated cartilage imaging is required after invasive cartilage repair procedures or conservative therapies, including pharmacological therapies, to monitor treatment effect. MR studies are required to tailor therapies and in the future new quantitative techniques may have significance in indicating treatment as well as monitoring therapy similar to bone mineral density currently used in the setting of osteoporosis.

Sign languages appear to be the major communication tool for the deaf community. As a minor commu... more Sign languages appear to be the major communication tool for the deaf community. As a minor community, Vietnamese deaf people often have to rely on a small numbers of interpreters who are hearing people knowing sign language in order to communicate with hearing people. It would be very beneficial for deaf as well as hearing people to develop an automated translation system between spoken/written languages and sign language. In this paper, we present our attempt to graphically decompose the gestures in Vietnamese Sign Language so that they can be easily synthesized in a 3D conversational agent. In order to describe the signs in Vietnamese Sign Language, we proposed an animation-level markup language. Based on this, we presented our 3D conversational agent for presenting multi-modal information for deaf people. The 3D agent can assist deaf people easier and in a more natural way.

Cerebrovascular Diseases, 2009

The diagnosis of external borderzone infarction is made when the stroke is located at the border ... more The diagnosis of external borderzone infarction is made when the stroke is located at the border between the arterial territories. Recent studies have raised questions regarding the location of this borderzone given the variability in the arterial territories. We examined the location of this region using a digital approach and its correspondence with the 'traditional' template. Infarcts resulting from occlusion of the middle cerebral artery (MCA) or posterior cerebral artery (PCA) trunk or branches were segmented from T(2)-weighted MR images and linearly registered into a common stereotaxic coordinate space. For MCA infarcts and PCA infarcts, maps of voxels in a rim surrounding the infarct were created. The maps of individual rims were averaged to create images of the probability of each voxel lying in the MCA and PCA rims. The MCA and PCA rims were used to create a digital atlas of the probability of each voxel lying concurrently in both rims. The MCA group consisted of 36 patients (16 males) with a median age of 73 (range 25-87) years. The PCA territory group consisted of 30 patients (24 males) with a median age of 61 (range 22-86) years. The probability of involvement in the digital atlas was higher in the posterior putamen (probability 0.12-0.29) and optic tract (probability 0.13-0.0.20) than in the angular gyrus (probability 0.01). We have created a digital model of the border region between the MCA and PCA territories. This approach may be useful for evaluating the likelihood of a stroke mechanism from topography.

Near-field aperture probes with high optical transmittance efficiency for optical recording and m... more Near-field aperture probes with high optical transmittance efficiency for optical recording and multi-probes with a metal wire as a heater for thermal recording are batch-fabricated by silicon micromachining. The aperture with diameter sizes from 10 to 500 nm at the apex of a SiO/sub 2/ tip on a Si cantilever is fabricated using a "Low temperature Oxidation & Selective Etching" technique. The SiO/sub 2/ tip is formed by nonuniform Si wet oxidation at 950/spl deg/C. The aperture is created at the apex of SiO/sub 2/ tip by selective etching SiO/sub 2/ in a buffered-HF. The aperture shows a high optical transmittance because the SiO/sub 2/ tip has a large opening angle. This fabrication technique is extended to fabricate a metal nanowire at the apex of the SiO/sub 2/ tip by embedding a metal into the aperture. By flowing a current into the metal wire, the tip can be heated. This probe array is fabricated, and the basic characteristics are evaluated.

Pediatric Nephrology, 2003

Autosomal recessive polycystic kidney disease (ARPKD) is a relatively common form of pediatric po... more Autosomal recessive polycystic kidney disease (ARPKD) is a relatively common form of pediatric polycystic kidney disease with an incidence of 1:20,000 live births. Previous reports, primarily from populations of European origin, indicate that the clinical presentation and disease course are quite variable. Using a retrospective study design, we sought to determine whether the clinical course and outcome of our multi-ethnic patient cohort differs from the published literature. A 10-year (1990–2000) retrospective study was conducted in which we reviewed the clinical, histopathological, and imaging records of our 31 ARPKD patients. Patients were diagnosed between 0 and 14 years of age, with 17 (55%) presenting within the 1st month of life. The mean follow-up was 67 months and age at last follow-up ranged from 0.5 to 16 years. Of the 17 patients diagnosed as neonates, 11 (65%) had respiratory insufficiency complicated by pneumothoraces. Two died shortly after birth and 2 died within the 1st year of life due to respiratory failure. Among the 13 neonatal survivors, 7 (54%) developed progressive renal insufficiency, whereas 6 of 14 (43%) of those children who presented beyond 1 month of age developed renal insufficiency. Hypertension was present in 55% of our patients, with nearly all neonatal survivors requiring antihypertensive management. Evidence of portal hypertension was found in 10 (37%) of the 27 patients who survived the 1st year of life. In our multi-ethnic ARPKD cohort, the 1-year survival rate (87%) and the clinical variability are comparable to those previously reported. With the recent identification of the PKHD1 gene, characterization of disease-causing mutations should provide new insights into the molecular basis for this phenotypic variability.

Rheologica Acta, 1999

Edge fracture is an instability of cone-plate and parallel plate flows of viscoelastic liquids an... more Edge fracture is an instability of cone-plate and parallel plate flows of viscoelastic liquids and suspensions, characterised by the formation of a `crack' or indentation at a critical shear rate on the free surface of the liquid. A study is undertaken of the theoretical, experimental and computational aspects of edge fracture. The Tanner-Keentok theory of edge fracture in second-order liquids is re-examined and is approximately extended to cover the Criminale-Ericksen-Filbey (CEF) model. The second-order theory shows that the stress distribution on the semi-circular crack is not constant, requiring an average to be taken of the stress; this affects the proportionality constant, K in the edge fracture equation −N 2c = KΓ/a, where N 2c is the critical second normal stress difference, Γ is the surface tension coefficient and a is the fracture diameter. When the minimum stress is used, K = 2/3 as found by Tanner and Keentok (1983). Consideration is given to the sources of experimental error, including secondary flow and slip (wall effect). The effect of inertia on edge fracture is derived. A video camera was used to record the inception and development of edge fracture in four viscoelastic liquids and two suspensions. The recorded image was then measured to obtain the fracture diameter. The edge fracture phenomenon was examined to find its dependence on the physical dimensions of the flow (i.e. parallel plate gap or cone angle), on the surface tension coefficient, on the critical shear rate and on the critical second normal stress difference. The critical second normal stress difference was found to depend on the surface tension coefficient and the fracture diameter, as shown by the theory of Tanner and Keentok (1983); however, the experimental data were best fitted by the equation −N 2c = 1.095Γ/a. It was found that edge fracture in viscoelastic liquids depends on the Reynolds number, which is in good agreement with the inertial theory of edge fracture. Edge fracture in lubricating grease and toothpaste is broadly consistent with the CEF model of edge fracture. A finite volume method program was used to simulate the flow of a viscoelastic liquid, obeying the modified Phan-Thien-Tanner model, to obtain the velocity and stress distribution in parallel plate flow in three dimensions. Stress concentrations of the second normal stress difference (N 2) were found in the plane of the crack; the velocity distribution shows a secondary flow tending to aid crack formation if N 2 is negative, and a secondary flow tending to suppress crack formation if N 2 is positive.

Geosciences Journal, 2009

To constrain the timing of collisional event in the Indochina block, SHRIMP U-Pb dating and REE a... more To constrain the timing of collisional event in the Indochina block, SHRIMP U-Pb dating and REE analyses of zircon were carried out for two paragneiss samples of the Kham Duc Complex, central Vietnam. Both samples contain kyanite, staurolite, and zoisite as relics from an early metamorphic stage (M1), and biotite and sillimanite as major minerals constituting the foliation formed during the late metamorphic stage (M2). The change in mineral assemblages indicates a clockwise P-T path composed of a high- or medium-P + low-T stage (M1) and a subsequent low- P + high-T stage (M2). The U-Pb concordia ages of zircon rims are 447 ± 6 Ma and 452 ± 6 Ma for the two samples, respectively. These results are distinctly different from the available Ar-Ar mineral ages of 254–225 Ma. Following the clockwise P-T path and phase equilibrium analyses of the Complex, we suggest that the zircon rims were formed near peak temperatures during the decompression. The ∼450 Ma zircon rim thus gives the minimum age constraint for a possible crustal thickening event during Early Paleozoic, whereas the reported Permo-Triassic Ar-Ar ages would result from an Indosinian overprint. This Early Paleozoic event is most likely related to a collisional orogeny between the Indochina and South China blocks. Late Neoproterozoic to Neoarchean ages are recorded from detrital zircon cores of the Kham Duc Complex, the Kontum Massif and Truong Son Belt, suggesting that their protoliths might have derived from sediments at the Gondwana margin.

Rheologica Acta, 2007

Flow instability in three entangled polymer systems including a 10 wt% 1,4-polybutadiene (PBD) so... more Flow instability in three entangled polymer systems including a 10 wt% 1,4-polybutadiene (PBD) solution, an 11.4 wt% polyisobutylene (PIB) solution, and a long chain branched polyethylene melt (LD 146) was investigated in both stress-controlled and rate-controlled experiments in the cone–plate geometry. It was found that flow instability occurred for experiments in both rate- and stress-controlled modes. The effects of cone angle or rim gap and shearing time on flow instability were studied. The smaller cone angle and shorter shearing time delay (in terms of stress or shear rate) the occurrence of severe instability and mass loss of the PBD solution but not for the PIB. Our data are consistent with the dramatic shear rate jump for the flow curve constructed from the stress-controlled experiments being associated with mass loss after the severe instabilities. We also find that the Cox–Merz representation gives a powerful tool for investigation of flow instability. Finally, another interesting result in this work is that it seems that the stress overshoot can be related to the onset of flow instability in the present system.

Journal of Electrostatics, 1997

Surface waves on a thin oil film placed on top of a ground-supported dielectric sheet has recentl... more Surface waves on a thin oil film placed on top of a ground-supported dielectric sheet has recently been observed to exist when the oil film has been precharged adequately and when a sharp grounded electrode is suddenly introduced into the vicinity of the oil layer .

Expert Systems With Applications

As new high-throughput technologies have created an explosion of biomedical literature, there ari... more As new high-throughput technologies have created an explosion of biomedical literature, there arises a pressing need for automatic information extraction from the literature bank. To this end, biomedical named entity recognition (NER) from natural language text is indispensable. Current NER approaches include: dictionary based, rule based, or machine learning based. Since there is no consolidated nomenclature for most biomedical NEs, any NER system relying on limited dictionaries or rules does not seem to perform satisfactorily. In this paper, we consider a machine learning model, CRF, for the construction of our NER framework. CRF is a well-known model for solving other sequence tagging problems. In our framework, we do our best to utilize available resources including dictionaries, web corpora, and lexical analyzers, and represent them as linguistic features in the CRF model. In the experiment on the JNLPBA 2004 data, with minimal postprocessing, our system achieves an F-score of 70.2%, which is better than most state-of-the-art systems. On the GENIA 3.02 corpus, our system achieves an F-score of 78.4% for protein names, which is 2.8% higher than the next-best system. In addition, we also examine the usefulness of each feature in our CRF model. Our experience could be valuable to other researchers working on machine learning based NER.

The most important clinical indications for magnetic resonance imaging (MRI) are assessment of ca... more The most important clinical indications for magnetic resonance imaging (MRI) are assessment of cartilage in osteoarthritis (OA), chronic or acute osteochondral injury including sports injuries, osteochondritis dissecans, chondromalacia patellae, and inflammatory arthropathies (in particular before invasive therapy). In addition dedicated cartilage imaging is required after invasive cartilage repair procedures or conservative therapies, including pharmacological therapies, to monitor treatment effect. MR studies are required to tailor therapies and in the future new quantitative techniques may have significance in indicating treatment as well as monitoring therapy similar to bone mineral density currently used in the setting of osteoporosis.

Sign languages appear to be the major communication tool for the deaf community. As a minor commu... more Sign languages appear to be the major communication tool for the deaf community. As a minor community, Vietnamese deaf people often have to rely on a small numbers of interpreters who are hearing people knowing sign language in order to communicate with hearing people. It would be very beneficial for deaf as well as hearing people to develop an automated translation system between spoken/written languages and sign language. In this paper, we present our attempt to graphically decompose the gestures in Vietnamese Sign Language so that they can be easily synthesized in a 3D conversational agent. In order to describe the signs in Vietnamese Sign Language, we proposed an animation-level markup language. Based on this, we presented our 3D conversational agent for presenting multi-modal information for deaf people. The 3D agent can assist deaf people easier and in a more natural way.

Cerebrovascular Diseases, 2009

The diagnosis of external borderzone infarction is made when the stroke is located at the border ... more The diagnosis of external borderzone infarction is made when the stroke is located at the border between the arterial territories. Recent studies have raised questions regarding the location of this borderzone given the variability in the arterial territories. We examined the location of this region using a digital approach and its correspondence with the 'traditional' template. Infarcts resulting from occlusion of the middle cerebral artery (MCA) or posterior cerebral artery (PCA) trunk or branches were segmented from T(2)-weighted MR images and linearly registered into a common stereotaxic coordinate space. For MCA infarcts and PCA infarcts, maps of voxels in a rim surrounding the infarct were created. The maps of individual rims were averaged to create images of the probability of each voxel lying in the MCA and PCA rims. The MCA and PCA rims were used to create a digital atlas of the probability of each voxel lying concurrently in both rims. The MCA group consisted of 36 patients (16 males) with a median age of 73 (range 25-87) years. The PCA territory group consisted of 30 patients (24 males) with a median age of 61 (range 22-86) years. The probability of involvement in the digital atlas was higher in the posterior putamen (probability 0.12-0.29) and optic tract (probability 0.13-0.0.20) than in the angular gyrus (probability 0.01). We have created a digital model of the border region between the MCA and PCA territories. This approach may be useful for evaluating the likelihood of a stroke mechanism from topography.

Near-field aperture probes with high optical transmittance efficiency for optical recording and m... more Near-field aperture probes with high optical transmittance efficiency for optical recording and multi-probes with a metal wire as a heater for thermal recording are batch-fabricated by silicon micromachining. The aperture with diameter sizes from 10 to 500 nm at the apex of a SiO/sub 2/ tip on a Si cantilever is fabricated using a "Low temperature Oxidation & Selective Etching" technique. The SiO/sub 2/ tip is formed by nonuniform Si wet oxidation at 950/spl deg/C. The aperture is created at the apex of SiO/sub 2/ tip by selective etching SiO/sub 2/ in a buffered-HF. The aperture shows a high optical transmittance because the SiO/sub 2/ tip has a large opening angle. This fabrication technique is extended to fabricate a metal nanowire at the apex of the SiO/sub 2/ tip by embedding a metal into the aperture. By flowing a current into the metal wire, the tip can be heated. This probe array is fabricated, and the basic characteristics are evaluated.