Biomedical subjects

Timothy Booth

Publications and source records attributed to Timothy Booth.

6 recordsLinked to original sources

PubMed2025

Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly.

MOTIVATION: De novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. RESULTS: Here, we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using Pacific Biosciences HiFi, Hi-C, and optionally Oxford Nanopore Technologies reads as input. Colora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies. AVAILABILITY AND IMPLEMENTATION: The source code of Colora is available on GitHub (https://github.com/LiaOb21/colora) and has been deposited in Zenodo under DOI https://doi.org/10.5281/zenodo.13321576. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/? usage=LiaOb21%2Fcolora).

Software↗

PubMed2005

Advantages of magnetic resonance imaging over computed tomography in preoperative evaluation of pediatric cochlear implant candidates.

OBJECTIVES: To compare magnetic resonance imaging (MRI) to high-resolution computed tomography (HRCT) in the preoperative evaluation of pediatric cochlear implant candidates. METHODS: The charts of pediatric cochlear implant candidates evaluated between July 1, 2000 and November 30, 2003 with an MRI scan of the inner ear were included in the study. Fifty-six patients were included. Associated HRCT scans were examined. Abnormalities of the cochlea, cochlear nerve, endolymphatic sac, endolymphatic duct, vestibule, and modiolus were noted. A pediatric neuroradiologist gave an opinion as to whether patients with anomalies seen with MRI but without associated HRCT would have been identified by HRCT. RESULTS: Of the 112 temporal bones imaged with MRI, the following abnormalities were encountered: 32% (36/112) had abnormalities of the cochlear turns, 30% (34/112) had abnormal signal in the modiolus, 23% (26/112) had abnormal vestibulae, 16% (18/112) had abnormal endolymphatic ducts, 15% (17/112) had abnormal endolymphatic sacs, 12% (13/112) had abnormalities of the cochlear nerves, 29% (17/56) had abnormalities of the brain. HRCT cannot directly evaluate the cochlear nerve. Available HRCT findings were combined with radiologic opinion and compared with MRI findings. The percentages of abnormalities identifiable by HRCT when compared with those seen with MRI are cochlea 42% (15/36), modiolus 35% (12/34), vestibulae 88% (23/26), endolymphatic duct 100% (18/18), and endolymphatic sac 6% (1/17). CONCLUSION: MRI is more sensitive and specific in diagnosing soft tissue abnormalities in the inner ear than HRCT in cochlear implant candidates (Fig. 4). Moreover, the abnormalities detected with MRI are more likely to influence the implantation process (e.g., asymmetric nerve aplasia, cochlear obstruction). (Figure is included in full-text article).

Child↗

PubMed2005

MR venography in the pediatric patient.

BACKGROUND AND PURPOSE: Little is known about age-related changes in posterior fossa venous anatomy on 2D time-of-flight MR venography (MRV) or about artifacts that limit its accuracy in diagnosing venous occlusive disease. We evaluated pediatric appearances of posterior fossa venous drainage. METHODS: One hundred and eight children with normal MR imaging or minimal congenital anomalies underwent 2D MRV. Transverse sinus dominance and absence and the presence of an occipital sinus were correlated with age. Venous structure conspicuity was compared on source and maximum intensity projection images. RESULTS: Right, left, and codominance of the transverse sinus, respectively, was as follows: at < 25 months, 37%, 21%, and 42%; 25 months to 5 years, 35%, 30%, 35%; and > or =6 years, 50%, 16%, 34%. Transverse sinus dominance was not related to age between the three groups (P=.58, chi-square contingency), but some relationship was observed when patients <6 years were compared to those > or =6 years (P=.032). Chi-square trends showed a mildly positive correlation between age and an absent transverse sinus (P=.026) and a decreasing trend in the presence of an occipital sinus with age (P=.038). Saturation effects due to in-plane/slow flow were worse in patients <25 months; effects in the transverse sinuses or internal jugular veins were miminized with coronal or axial imaging, respectively. CONCLUSION: 2D TOF MRV shows age-related changes in venous anatomy. Caution should be used before posterior fossa venous occlusive disease is diagnosed on the basis of signal intensity loss, especially in neonates and young infants.

Adolescent↗

PubMed2003

Skip metastasis in osteosarcoma.

Skip metastasis is rare in high-grade osteosarcoma and indicates a very poor prognosis. The authors describe two patients who had high-grade osteosarcoma and skip metastasis. MRI detected the skip lesion in both patients, and both lesions were confirmed by histology. The patients were treated with adjuvant chemotherapy and radical surgical resection. Both are alive and free of disease 3 and 6 years from diagnosis.

Adolescent↗

PubMed2002

Nonperioperative strokes in children with central nervous system tumors.

BACKGROUND: Nonperioperative strokes are rare yet potentially devastating events for children with central nervous system (CNS) tumors. The incidence of and risk factors for nonperioperative strokes in children with CNS tumors is unknown. METHODS: The authors performed a retrospective review of children from their institution with CNS tumors. The incidence of stroke in the nonperioperative period and the influence of patient demographic factors, coexisting genetic diseases, tumor type, and treatment modality on the subsequent occurrence of a stroke were determined. RESULTS: Eight hundred seven consecutive patients from the authors' institution with CNS tumors were observed for a combined 3224 nonperioperative years. Thirteen patients (1.6%) had a nonperioperative stroke, for an incidence of 4.03 strokes/1000 years of nonperioperative patient follow-up. Eight patients were males, and the median age at diagnosis of a CNS tumor was 4.8 years (range, 0.3-18.6 years). The median duration from diagnosis of a CNS tumor until the occurrence of stroke was 2.3 years (range, 0.3-15.8 years). Among numerous potential risk factors individually examined by chi-square analysis, only treatment with radiation therapy was associated with the subsequent development of a stroke (chi-square, P = 0.007). By logistic regression analysis, treatment with radiation therapy and a diagnosis of an optic pathway glioma were the only statistically significant variables associated with a stroke. CONCLUSIONS: Strokes are much more common among children with CNS tumors. Children treated with radiation therapy and those with optic pathway gliomas have a higher association with the occurrence of a subsequent nonperioperative stroke. Because children with optic pathway gliomas may be at particularly high risk of stroke after radiation therapy, the desired beneficial therapeutic effects of irradiation must always be weighed against its potentially adverse effects, including stroke.

Adolescent↗

PubMedDate not supplied

Acute methotrexate neurotoxicity: findings on diffusion-weighted imaging and correlation with clinical outcome.

BACKGROUND AND PURPOSE: Acute lymphocytic leukemia (ALL) is a common malignancy of childhood treated with methotrexate (MTX), which is associated with acute neurotoxicity. We evaluated diffusion-weighted (DW) and conventional MR images in children with ALL and acute MTX-induced neurotoxicity, with clinical correlation. METHODS: Five patients aged 12-15 years underwent fluid-attenuated inversion recovery (FLAIR), T2-weighted fast spin-echo and gradient-echo, T1-weighted gadolinium-enhanced spin-echo, and DW imaging within 24 hours of symptom onset. Records were reviewed for the temporal relationship to MTX administration, strokelike symptoms, and neurologic outcome. RESULTS: Six strokelike events were temporally related to intrathecal MTX given 6-11 days before symptom onset. FLAIR images showed abnormal hyperintensity in the callosal splenium in one patient but were otherwise normal. Diffusion abnormalities were frontoparietal in three events and frontal in one; nonfluent aphasia was seen in all. Bilateral frontoparietal diffusion abnormalities were associated with bilateral upper-extremity weakness, right-sided hemiparesis, or left-sided hemiparesis (one patient each); one patient had mild facial droop. Unilateral precentral subcortical diffusion abnormality was associated with contralateral motor deficit and ipsilateral upper-extremity sensory loss. Strokelike symptoms resolved rapidly and were not associated with other signs of encephalopathy. Subsequent intrathecal MTX administration was not associated with recurrence in four patients. CONCLUSION: Diffusion abnormalities in acute MTX neurotoxicity indicated cerebral dysfunction but not necessarily overt structural injury to the cerebrum. Subsequent demyelination or gliosis could not be predicted on the basis of diffusion abnormalities. A single strokelike episode with diffusion abnormalities should not necessarily prompt modification of potentially curative chemotherapeutic regimens.

Acute Disease↗