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1.  Generic Feature Selection with Short Fat Data 
Consider a regression problem in which there are many more explanatory variables than data points, i.e., p ≫ n. Essentially, without reducing the number of variables inference is impossible. So, we group the p explanatory variables into blocks by clustering, evaluate statistics on the blocks and then regress the response on these statistics under a penalized error criterion to obtain estimates of the regression coefficients. We examine the performance of this approach for a variety of choices of n, p, classes of statistics, clustering algorithms, penalty terms, and data types. When n is not large, the discrimination over number of statistics is weak, but computations suggest regressing on approximately [n/K] statistics where K is the number of blocks formed by a clustering algorithm. Small deviations from this are observed when the blocks of variables are of very different sizes. Larger deviations are observed when the penalty term is an Lq norm with high enough q.
PMCID: PMC4208697  PMID: 25346546
Large p small n; LASSO; Ridge; Bridge; Clustering; Variance-bias tradeoff; Summary statistics
2.  Oncogenic K-Ras requires activation for enhanced activity 
Oncogene  2013;33(4):532-535.
Oncogenic Ras mutations are widely considered to be locked in a permanent ‘On’ state and ‘constitutively active’. Yet, many healthy people have cells possessing mutant Ras without apparent harm, and in animal models mutant Ras causes transformation only after upregulation of Ras activity. Here, we demonstrate that oncogenic K-Ras is not constitutively active but can be readily activated by upstream stimulants to lead to prolonged strong Ras activity. These data indicate that in addition to targeting K-Ras downstream effectors, interventions to reduce K-Ras activation may have important cancer-preventive value, especially in patients with oncogenic Ras mutations. As other small G proteins are regulated in a similar manner, this concept is likely to apply broadly to the entire Ras family of molecules.
PMCID: PMC3923400  PMID: 23334325
cancer; Ras-GTP
3.  Hypogonadism in Patients with Sickle Cell Disease: Central or Peripheral? 
Acta haematologica  2012;128(2):10.1159/000337344.
There is conflicting evidence in the literature on the etiology of hypogonadism in patients with sickle cell disease (SCD). A cross-sectional study was done to determine whether hypogonadism in male patients with SCD is due to primary testicular failure or secondary pituitary/hypothalamic dysfunction and assess the association between hypogonadism and serum ferritin levels. Hormonal assessment for serum concentrations of testosterone, follicle stimulating hormone (FSH) and luteinizing hormone (LH) was done for 34 men with SCD and their charts were reviewed for relevant clinical variables. Eight men (24%) were classified hypogonadal based on their serum testosterone levels. These men have significantly lower LH (p = 0.001) and FSH (p = 0.01) levels than normogonadal men, indicating a central etiology. There was no significant difference between hypogonadal and normogonadal men with respect to ferritin levels (p = 0.71). Our study indicates a central etiology of hypogonadism in patients with SCD. In this small study ferritin level was not significantly related to hypogonadism.
PMCID: PMC3864664  PMID: 22678347
Ferritin; Hemoglobinopathy; Hypogonadism; Testosterone
4.  FLAP pharmacological blockade modulates metabolism of endogenous tau in vivo  
Translational Psychiatry  2013;3(12):e333-.
FLAP (5-lipoxygenase-activating protein) is a protein widely distributed within the central nervous system whose function is to regulate the activation of the 5-Lipoxygenase enzyme. Although previous works show that pharmacological blockade of FLAP improve the amyloidotic phenotype of the Tg2576, its contribution to tau pathology remains to be investigated. In the present paper, we studied the effect of FLAP pharmacological inhibition on the metabolism of endogenous tau in these mice. Total tau levels in the brains of mice receiving MK-591, a selective and specific FLAP inhibitor, were not changed when compared with controls. By contrast, treated animals had a significant reduction of tau phosphorylation at specific sites: Ser396; Ser396/Ser404; and Thr 231/Ser 235. This reduction was associated with a significant decrease in the activity of glycogen synthase kinase-3 beta, but not other kinases. In addition, MK-591-treated mice had a significant increase in the post-synaptic density protein-95 and the dendritic protein microtubule-associated protein 2. These data establish a novel functional role for FLAP in the metabolism of tau, and together with its known Aβ modulatory effect they suggest that its pharmacological inhibition could represent a novel therapeutic opportunity for Alzheimer's disease.
PMCID: PMC4030325  PMID: 24301651
Alzheimer's disease; amyloid; FLAP protein; transgenic animal models; tau protein
5.  Dual-source, dual-energy multidetector CT for the evaluation of pancreatic tumours 
The British Journal of Radiology  2012;85(1018):e891-e898.
To investigate the potential diagnostic value of dual-energy CT (DECT) with virtual non-enhanced (VNE) and iodine-only images, and to determine the optimal mixed ratio of blended images for evaluation of pancreatic diseases.
Multiphasic DECT was performed in 44 patients with focal pancreatic disease. DECT was used during the pancreatic and hepatic venous phases, and a peak kilovoltage of 120 kVp was used for both non-contrast phases. For qualitative analysis of the CT images, two radiologists assessed three image sets (VNE, iodine-only and blended images) in order to determine the acceptability of VNE in replacing true non-enhanced (TNE) images, the added value of iodine-only images and the preferred blending ratio. For quantitative analyses, the CT numbers and image noise of the pancreatic parenchyma, lesions, aorta and psoas muscle were measured. The contrast-to-noise ratio of the lesion was calculated on the pancreatic phase images. The effective radiation dose for DECT and TNE images was calculated. Statistical comparisons were made using the Friedman test, the Wilcoxon test, the paired t-test and repeated measures of analysis of variation with Bonferroni correction for multiple comparisons.
The level of acceptance of the VNE images in replacing TNE images was 90.9%. Regarding the iodine-only images, 50% of the cases were found to have an added value. The linear-blended images with a weighting factor of 0.5 were preferred.
DECT was able to provide high-quality VNE images that could replace TNE images and iodine-only images showing an added value. Blended images with a weighting factor of 0.5 were preferred by the reviewers.
PMCID: PMC3474024  PMID: 22972978
6.  Randomized Multicenter Clinical Trial of Myofascial Physical Therapy in Women with Interstitial Cystitis/Painful Bladder Syndrome (IC/PBS) and Pelvic Floor Tenderness 
The Journal of Urology  2012;187(6):2113-2118.
To determine the efficacy and safety of pelvic floor Myofascial Physical Therapy (MPT) in women with newly-symptomatic IC/PBS, as compared to Global Therapeutic Massage (GTM).
Materials and Methods
A randomized controlled trial of 10 scheduled treatments of MPT vs. GTM was performed at 11 clinical centers located in North America. We recruited women with IC/PBS with demonstrable pelvic floor tenderness on physical examination and a limitation of no more than 3 years symptom duration. The primary outcome was the proportion of responders defined as ‘moderately improved’ or ‘markedly improved’ in overall symptoms compared to baseline on a 7-point scale Global Response Assessment (GRA). Secondary outcomes included ratings for pain, urgency, frequency; the O'Leary-Sant IC Symptom and Problem Index (ICSI/ICPI) and reports of adverse events. We compared response rates between treatment arms using the exact conditional version of the Mantel-Haenszel test to control for clustering by clinical center. For secondary efficacy outcomes, cross-sectional descriptive statistics and changes from baseline were calculated.
Eighty-one women randomized to the two treatment groups had similar symptoms at baseline. The GRA response rate was 26% in the GTM group and 59% in the MPT group (p=0.0012). Pain, urgency, and frequency ratings and in ICSI/ICPI decreased in both groups during follow-up and were not significantly different between the groups. Pain was the most common adverse event, occurring at similar rates in both groups. There were no serious adverse events reported.
A significantly higher proportion of women with IC/PBS reponded to treatment with MPT than with GTM. MPT may be a beneficial therapy in women with this syndrome.
PMCID: PMC3351550  PMID: 22503015
Urologic Pelvic Pain Syndrome; Interstitial Cystitis; Painful Bladder Syndrome; Physical Therapy
7.  Pituicytoma: case report and literature review 
The British Journal of Radiology  2011;84(999):e055-e057.
Pituicytoma is a rare primary tumour of the neurohypophysis or infundibulum, which masquerades as a pituitary adenoma. We present a pituicytoma case in a 45-year-old female presenting as a focal lesion of the neurohypophysis. This case report reviews the clinical, neuroimaging and histopathological features of this rare tumour in order to understand it better.
PMCID: PMC3473875  PMID: 21325358
8.  Colonic phytobezoar 
BMJ Case Reports  2009;2009:bcr2006039412.
PMCID: PMC3034740  PMID: 21687062
9.  Double wall sign 
BMJ Case Reports  2009;2009:bcr2006039149.
PMCID: PMC3034752  PMID: 21687060
10.  Haemoptysis from the pulmonary artery 
BMJ Case Reports  2009;2009:bcr2006039172.
PMCID: PMC3034759  PMID: 21687061
11.  Tumoral calcinosis of bilateral hip 
BMJ Case Reports  2009;2009:bcr2007050450.
PMCID: PMC3034765  PMID: 21687251
12.  Gas-forming Ludwig’s angina 
BMJ Case Reports  2009;2009:bcr2006045922.
PMCID: PMC3034785  PMID: 21687088
13.  Persistent flank pain without active urinary sediments 
BMJ Case Reports  2009;2009:bcr2006037556.
PMCID: PMC3034825  PMID: 21687054
14.  Colonic phytobezoar 
PMCID: PMC2658416  PMID: 17582058
15.  Double wall sign 
PMCID: PMC2658417  PMID: 17582057
16.  Persistent flank pain without active urinary sediments 
PMCID: PMC2658297  PMID: 17513557
17.  The great fortune of misfortune 
PMCID: PMC2564269  PMID: 17130614
maxillofacial injury; penetrating wound
18.  Listerial meningitis in a patient with undiagnosed acquired immunodeficiency syndrome: ampicillin should be added to the empirical antibiotic coverage 
Meningitis is an important differential diagnosis in patients with fever, headache, and/or altered consciousness in the emergency department (ED). With human immunodeficiency virus (HIV) infection becoming increasingly common, patients with acquired immunodeficiency syndrome (AIDS) need to be recognised promptly to facilitate the choice of appropriate antibiotic therapy for potential opportunistic infections. Physicians should be able to recognise a patient with undiagnosed AIDS who presents to the ED and perform further confirmational tests without violating the rights of the patient. Additional tests focusing on discovering potential opportunistic pathogens should be performed. Ampicillin should be added to the empirical regimen for the coverage of Listeria meningocerebritis, which should be considered in all potentially immunocompromised hosts with suggestive clinical presentations. Failure to recognise patients with AIDS and provide antibiotics active against L monocytogenes in such hosts may lead to a catastrophic outcome.
PMCID: PMC2564238  PMID: 16921071
Listeria monocytogenes ; meningitis; myocarditis; acquired immunodeficiency syndrome; human immunodeficiency virus
19.  Electrical twitch obtaining intramuscular stimulation (ETOIMS) for myofascial pain syndrome in a football player 
Case report: An elite American football player with MPS symptoms failed to respond to standard treatments. He then received ETOIMS which completely alleviated the pain. After establishing pain control, the athlete continued with a further series of treatments to control symptoms of muscle tightness.
Conclusions: ETOIMS has a promising role in pain alleviation, increasing and maintaining range of motion, and in providing satisfactory athletic performance during long term follow up.
PMCID: PMC1724955  PMID: 15388569
20.  Online Annotation Tool for Dental Radiology 
Dental imaging plays a significant role in the process of diagnoses of oral cancer. In this project, an online annotation tool for dental radiology is developed to support systematic annotation, which includes image findings, descriptive information on the lesion, patient characteristics and pathology data. This tool will be available for the dental schools in US who are interested in the creation of dental image archives for teaching and research.
PMCID: PMC1560787  PMID: 16779419
21.  Infectious Entry of West Nile Virus Occurs through a Clathrin-Mediated Endocytic Pathway 
Journal of Virology  2004;78(19):10543-10555.
The pathway of West Nile flavivirus early internalization events was mapped in detail in this study. Overexpression of dominant-negative mutants of Eps15 strongly inhibits West Nile virus (WNV) internalization, and pharmacological drugs that blocks clathrin also caused a marked reduction in virus entry but not caveola-dependent endocytosis inhibitory agent, filipin. Using immunocryoelectron microscopy, WNV particles were seen within clathrin-coated pits after 2 min postinfection. Double-labeling immunofluorescence assays and immunoelectron microscopy performed with anti-WNV envelope or capsid proteins and cellular markers (EEA1 and LAMP1) revealed the trafficking pathway of internalized virus particles from early endosomes to lysosomes and finally the uncoating of the virus particles. Disruption of host cell cytoskeleton (actin filaments and microtubules) with cytochalasin D and nocodazole showed significant reduction in virus infectivity. Actin filaments are shown to be essential during the initial penetration of the virus across the plasma membrane, whereas microtubules are involved in the trafficking of internalized virus from early endosomes to lysosomes for uncoating. Cells treated with lysosomotropic agents were largely resistant to infection, indicating that a low-pH-dependent step is required for WNV infection. In situ hybridization of DNA probes specific for viral RNA demonstrated the trafficking of uncoated viral RNA genomes to the endoplasmic reticulum.
PMCID: PMC516396  PMID: 15367621
22.  Intraoperative radiation therapy as an adjunctive therapy for huge and highly vascular parasagittal meningiomas. 
Journal of Korean Medical Science  2000;15(6):718-723.
This case presents a 34-year-old man who had a huge parasagittal meningioma. Initial treatment consisted of preoperative external carotid artery embolization and partial tumor resection. During the resection, we found that the tumor invaded the adjacent calvarium, and due to massive hemorrhage, total removal of the tumor was impossible. The patient was treated with intraoperative radiation therapy (IORT) (25 Gy via 16 MeV) as an adjunctive therapy. Eight months after IORT, we were able to remove the tumor completely without surgical difficulties. IORT can be considered an useful adjunctive therapy for the superficially located, huge, and highly vascular meningioma.
PMCID: PMC3054693  PMID: 11194202
23.  Blockade of CD49d (alpha4 integrin) on intrapulmonary but not circulating leukocytes inhibits airway inflammation and hyperresponsiveness in a mouse model of asthma. 
Journal of Clinical Investigation  1997;100(12):3083-3092.
Immunized mice after inhalation of specific antigen have the following characteristic features of human asthma: airway eosinophilia, mucus and Th2 cytokine release, and hyperresponsiveness to methacholine. A model of late-phase allergic pulmonary inflammation in ovalbumin-sensitized mice was used to address the role of the alpha4 integrin (CD49d) in mediating the airway inflammation and hyperresponsiveness. Local, intrapulmonary blockade of CD49d by intranasal administration of CD49d mAb inhibited all signs of lung inflammation, IL-4 and IL-5 release, and hyperresponsiveness to methacholine. In contrast, CD49d blockade on circulating leukocytes by intraperitoneal CD49d mAb treatment only prevented the airway eosinophilia. In this asthma model, a CD49d-positive intrapulmonary leukocyte distinct from the eosinophil is the key effector cell of allergen-induced pulmonary inflammation and hyperresponsiveness.
PMCID: PMC508521  PMID: 9399955
24.  Preliminary experiences with intraoperative radiation therapy (IORT) for the treatment of brain tumors. 
Journal of Korean Medical Science  1995;10(6):449-452.
Ten brain tumor patients underwent wide resection of the tumor followed by Intraoperative Radiation Therapy (IORT) at the first surgery or at the second salvage surgery after failure of conventional external beam irradiation. Two patients(1 meningioma, 1 glioblastoma multiforme) were treated at the first surgery and 8 patients(3 anaplastic astrocytoma, 3 glioblastoma multiforme, 1 meningioma, 1 gliosarcoma) were treated after salvage surgery. The IORT doses were ranged from 15-25 Gy depending on the tumor volume and previous radiation therapy. The neurological status(Karnofsky performance status) was improved in 4 cases, not changed in 6 cases after IORT. There were several complications after IORT; radiation necrosis, communicating hydrocephalus, wound infection, and abnormal CT findings such as diffuse low density area in an around operation site. The radiation necrosis was confirmed by operation in a recurrent meningioma patient 12 months after IORT. At follow-up, ranging from 1 to 16 months, there was no deaths. Based on our limited experiences, the IORT might be one of the adjuvant therapeutic modalities especially for the malignant brain tumors and unresectable huge meningioma.
PMCID: PMC3053885  PMID: 8924231
25.  Relationship between tissue plasminogen activator, plasminogen activator inhibitor and CT image in chronic subdural hematoma. 
Journal of Korean Medical Science  1995;10(5):373-378.
The present study was performed to investigate the relationship between the concentrations of tissue-type plasminogen activator (t-PA) and plasminogen activator inhibitor (PAI) and the CT images in 23 cases of chronic subdural hematomas (SDHs). The concentrations of t-PA and PAI-1 were quantified by enzyme-linked immunosorbent assay (ELISA). Chronic SDHs were divided into five groups according to their appearance on computed tomography: high-density (n = 4), isodensity (n = 8), low-density (n = 5), mixed-density (n = 3), layering (n = 3) types. The volume of hematoma was measured with an image analyzing software program. The concentrations of t-PA were higher in layering (41.2 +/- 0.3 ng/ml, mean +/- standard error of the mean) and high-density (40.0 +/- 1.1 ng/ml) types compared to those of low-density (23.3 +/- 4.1 ng/ml) and iso-density (25.1 +/- 3.7 ng/ml) types. The concentrations of PAI-1 were lower in layering (95.9 +/- 1.0 ng/ml) and high-density (103.4 +/- 34.5 ng/ml) types compared to that of low-density (192.5 +/- 2.6 ng/ml) type. So the ratio between t-PA and PAI-1 (t-PA/PAI) was greater in layering and high-density types. The volume of hematoma was larger in mixed-density and layering types but statistically insignificant. These results presumably suggest that the ratio between t-PA and PAI concentration may contribute to the pathogenesis of the chronic SDH.
PMCID: PMC3054143  PMID: 8750064

Results 1-25 (32)