Biomedical subjects

John Lin

Publications and source records attributed to John Lin.

12 recordsLinked to original sources

PubMed2006

BioNetBuilder: automatic integration of biological networks.

UNLABELLED: BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases. Users can create networks for approximately 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others. The BioNetBuilder plugin client is available as a Java Webstart, providing a platform-independent network interface to these public databases. AVAILABILITY: http://err.bio.nyu.edu/cytoscape/bionetbuilder/

Algorithms↗

PubMed2006

Lateral gene transfer in vitro in the intracellular pathogen Chlamydia trachomatis.

Genetic recombinants that resulted from lateral gene transfer (LGT) have been detected in sexually transmitted disease isolates of Chlamydia trachomatis, but a mechanism for LGT in C. trachomatis has not been described. We describe here a system that readily detects C. trachomatis LGT in vitro and that may facilitate discovery of its mechanisms. Host cells were simultaneously infected in the absence of antibiotics with an ofloxacin-resistant mutant and a second mutant that was resistant to lincomycin, trimethoprim, or rifampin. Selection for doubly resistant C. trachomatis isolates in the progeny detected apparent recombinant frequencies of 10(-4) to 10(-3), approximately 10(4) times more frequent than doubly resistant spontaneous mutants in progeny from uniparental control infections. Polyclonal doubly resistant populations and clones isolated from them in the absence of antibiotics had the specific resistance-conferring mutations present in the parental mutants; absence of the corresponding normal nucleotides indicated that they had been replaced by homologous recombination. These results eliminate spontaneous mutation, between-strain complementation, and heterotypic resistance as general explanations of multiply resistant C. trachomatis that originated in mixed infections in our experiments and demonstrate genetic stability of the recombinants. The kind of LGT we observed might be useful for creating new strains for functional studies by creating new alleles or combinations of alleles of polymorphic loci and might also disseminate antibiotic resistance genes in vivo. The apparent absence of phages and conjugative plasmids in C. trachomatis suggests that the LGT may have occurred by means of natural DNA transformation. Therefore, the experimental system may have implications for genetically altering C. trachomatis by means of DNA transfer.

Anti-Bacterial Agents↗

PubMed2005

Treatment with trkC agonist antibodies delays disease progression in neuromuscular degeneration (nmd) mice.

Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a fatal autosomal recessive disorder seen in infants. It is characterized by lower motor neuron degeneration, progressive muscle paralysis and respiratory failure, for which no effective treatment exists. The phenotype of neuromuscular degeneration (nmd) mice closely resembles the human SMARD1. The identification of the mutated mouse gene in nmd mice, Ighmbp2, led to the discovery of mutations of the homologous gene in humans with SMARD1. We have studied the nmd mouse model with in vivo electrophysiological techniques and evaluated the efficacy of Mab2256, a monoclonal antibody with agonist effect on the tyrosine kinase receptor C, trkC, on disease progression in nmd mice. Treatment with Mab2256 resulted in a significant but transient improvement of muscle strength in nmd mice, as well as normalization of the neuromuscular depression during high-frequency nerve stimulation. These results suggest the potential of using monoclonal agonist antibodies for neurotrophin receptors in lower motor neuron diseases such as SMARD1.

Animals↗

PubMed2005

Analyzing and capturing articulated hand motion in image sequences.

Capturing the human hand motion from video involves the estimation of the rigid global hand pose as well as the nonrigid finger articulation. The complexity induced by the high degrees of freedom of the articulated hand challenges many visual tracking techniques. For example, the particle filtering technique is plagued by the demanding requirement of a huge number of particles and the phenomenon of particle degeneracy. This paper presents a novel approach to tracking the articulated hand in video by learning and integrating natural hand motion priors. To cope with the finger articulation, this paper proposes a powerful sequential Monte Carlo tracking algorithm based on importance sampling techniques, where the importance function is based on an initial manifold model of the articulation configuration space learned from motion-captured data. In addition, this paper presents a divide-and-conquer strategy that decouples the hand poses and finger articulations and integrates them in an iterative framework to reduce the complexity of the problem. Our experiments show that this approach is effective and efficient for tracking the articulated hand. This approach can be extended to track other articulated targets.

Algorithms↗

PubMed2004

Differential effects of nicotine on the activity of substantia nigra and ventral tegmental area dopaminergic neurons in vitro.

Despite resembling each other in many respects, dopaminergic neurons of the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) exhibit dissimilar responses to nicotine in vivo. To investigate this in an in vitro model, the acute effects of nicotine on the firing of SNc and VTA neurons were compared in transverse juvenile rat midbrain sections (300-350 microm) using extracellular recording. Levels of nicotine comparable with those encountered in smokers (0.2-1.0 microM, 3 min) not only increased firing rate, but also evoked prolonged irregular firing, as indicated by the increase in the coefficient of variation of discharge frequencies. Pre- and postsynaptic nicotinic cholinergic receptors (nAChRs) were involved, as both effects persisted, although at an attenuated level, in low Ca2+ / high Mg2+. Only the nicotine-induced elevation of firing rate was sensitive to the glutamate receptor antagonists APV and CNQX, implying that enhanced glutamate release and glutamate receptor activation are involved in the effects of nicotine on discharge frequency but not pattern. Furthermore, nicotine (1.0 microM) exerted a greater increase in the firing frequency of VTA neurons relative to SNc neurons, suggesting that the differential effects on the two populations previously reported in vivo were due to a difference in the postsynaptic nAChR response and/or local synaptic circuits. Low concentrations of nicotine can thus profoundly modulate the activity of dopaminergic mesencephalic neurons through a local action within the ventral midbrain in vitro, and, similarly to in vivo conditions, evoke stronger effects in the VTA.

Animals↗

PubMed2004

Bacteria in the treatment of cancer.

Incidental observations of cancer regression following spontaneous bacterial infection have led to the preclinical development of bacteria as potential therapeutics in the treatment of cancer. A variety of natural and gene-modified bacterial species have now been explored as potential cancer treatments. The selectivity of bacterial species towards cancer will be discussed, direct bacterial oncolytic activity will be summarized and the use of bacteria as gene and/or protein delivery vehicles will be described. Preclinical and early clinical results presented indicate a high safety profile and demonstrate clear anticancer activity, thereby justifying further investigation of bacteria as a therapeutic approach in the treatment of cancer.

Animals↗

PubMed2003

Limited effectiveness of sonography in revealing hip joint effusion: preliminary results in 21 adult patients with native and postoperative hips.

OBJECTIVE: The object of this study was to determine the effectiveness of sonography in the detection of hip joint effusions in both native and postoperative adult hips using arthrocentesis as a gold standard. MATERIALS AND METHODS: Twenty-one consecutive patients with clinical suspicion of hip joint effusion were examined on sonography by one of five musculoskeletal radiologists with experience in musculoskeletal sonography. All 21 patients underwent diagnostic arthrocentesis (fluoroscopic in 16, sonographic in five) to confirm the presence or absence of joint effusion. A retrospective analysis of the sonograms was made to assess the size of the distention of the anterior joint recess (anteroposterior dimension) and the echogenicity (anechoic or other relative to muscle), and correlation was made to the presence or absence of joint effusion. RESULTS: Joint effusion was seen on diagnostic arthrocentesis in 10 (48%) of the 21 patients. Seven of the 21 patients had native hips and 14 had prior hip surgery. Retrospectively, no significant difference was found with regard to the size of the anterior recess distention (p = 0.34) or echogenicity (p = 0.2) when comparing the patients with and without joint effusion. CONCLUSION: Anterior recess distention and echogenicity could not reliably be used as an indicator of adult hip joint effusion, either in native or postoperative hips. Diagnostic arthrocentesis was necessary to establish or exclude the presence of hip joint effusion.

Adult↗

PubMed2002

The network vs. pacemaker theory of the activity of RVL presympathetic neurons--a comparison with another putative pacemaker system.

Intracellular studies previously conducted in our laboratory on adult rats indicate that the activity of spinally projecting RVL neurons (neurons located in the Rostral Ventrolateral Medulla) results from synaptic inputs. The data obtained by others in medullary slices suggest that the firing of these neurons (RVL C1 and/or non-C1 type, depending on experimental conditions) is mainly determined by their 'beating' pacemaker properties. Interestingly, there is an analogy between the contrasting views on the role of the network vs. pacemakers in the generation of sympathetic tone, and a debate regarding the relative role of such mechanisms in other types of 'spontaneously' active neurons, including dopaminergic neurons of the Substantia Nigra/Ventral Tegmental Area (in ventral mesencephalon). This short review discusses our previous in vivo studies and more recent data obtained in vitro after acute cell isolation, showing that under both experimental conditions, the RVL neurons display no clear pacemaker-like properties. Interestingly, pacemaker activity of dopaminergic mesencephalic neurons can be easily demonstrated in brain slices and after acute isolation, but not in vivo. These findings strongly suggest that under normal in vivo conditions, individual neurons belonging to these two neural systems function as elements of networks.

Animals↗

PubMed2002

Sonography of ankle Ganglia with pathologic correlation in 10 pediatric and adult patients.

OBJECTIVE: We describe the sonographic imaging characteristics of ankle ganglia with pathologic correlation in 10 patients. CONCLUSION: Foot and ankle ganglia exhibit a spectrum of sonographic appearances from round and completely anechoic masses to hypoechoic, multilobulated, multiseptated masses with dependent debris. All the ganglionic cysts examined in our study showed posterior acoustic enhancement without solid nodules on sonography.

Adolescent↗

PubMed2002

Sonography of ankle tendon impingement with surgical correlation.

OBJECTIVE: This report describes sonography of ankle tendon impingement due to osteophytes, fracture fragments, and orthopedic hardware. CONCLUSION: Sonography can be helpful in identifying ankle tendon impingement due to osteophytes, fracture fragments, and orthopedic hardware. In such cases, dynamic sonography can aid assessment.

Adult↗

PubMedDate not supplied

Improving educational computer exhibits at radiologic meetings by modifying computer environment: results of an observational study.

An observational study of educational computer exhibits (ECEs) at the 86th Scientific Assembly and Annual Meeting of the Radiological Society of North America in 2000 was performed to determine the frequency with which the ECEs were in working order. At any given time, an average of 10% of the 71 exhibits were found to be inoperable, and, although some exhibits were functioning 100% of the time, others were not functioning up to 55% of the time. These observations underscore the importance of careful design when creating a computer-based exhibit for a meeting. Downtime of ECEs at meetings is the result of both intentional and unintentional user actions. Given that traditional poster presentations are "working" 100% of the time, modifications made to the environment of an exhibit computer to reduce downtime would be beneficial. Several relatively easy computer configuration steps can be taken that will likely improve the amount of time that an exhibit is functional. Electronic exhibits allow a more interactive experience for users and, with some assistance, will continue to be an effective educational tool.

Audiovisual Aids↗

PubMedDate not supplied

Aids to successful shoulder arthrography performed with a fluoroscopically guided anterior approach.

One method for performing effective shoulder arthrography with a fluoroscopically guided anterior approach is described. The technique can ensure success while injury to the cartilaginous labrum is avoided, which is essential when arthrography is performed in conjunction with magnetic resonance (MR) imaging. The key features of the technique include supine positioning of the patient with the shoulder in external rotation, marking the skin just lateral to the humeral head cortex, inserting the needle perpendicular to the fluoroscopy beam, testing the injection with an anesthetic agent, and confirming intraarticular needle placement with iodinated contrast material. The procedure can be followed by an injection of dilute gadolinium solution for subsequent MR imaging. Proper patient and needle positioning as well as accurate confirmation of intraarticular needle placement are critical to a successful and atraumatic shoulder arthrographic examination.

Adolescent↗