Recent Stanford Publications in PubMed
- Atypia of Undetermined Significance and Follicular Lesions of Undetermined Significance: Sonographic Assessment for Prediction of the Final Diagnosis.Kamaya A, Lewis GH, Liu Y, Akatsu H, Kong C, Desser TSJ Ultrasound Med
- Solving the puzzle of human warfare requires an explanation of battle raids and cultural institutions.Zefferman MR, Baldini R, Mathew SProc Natl Acad Sci U S A
- Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.Lee J, Taylor SE, Smeriglio P, Lai J, Maloney WJ, Yang F, Bhutani NFASEB J
- Perioperative Management of Diabetic Patients Undergoing Hand Surgery.Kang JR, Yao JJ Hand Surg Am
- Obsessional Disorders in al-Balkhi's 9th century treatise: Sustenance of the Body and Soul.Awaad R, Ali SJ Affect Disord
- The MGMT promoter SNP rs16906252 is a risk factor for MGMT methylation in glioblastoma and is predictive of response to temozolomide.Rapkins RW, Wang F, Nguyen HN, Cloughesy TF, Lai A, Ha W, Nowak AK, Hitchins MP, McDonald KLNeuro Oncol
- Preparing to take the USMLE Step 1: a survey on medical students' self-reported study habits.Kumar AD, Shah MK, Maley JH, Evron J, Gyftopoulos A, Miller CPostgrad Med J
- A pooling-based approach to mapping genetic variants associated with DNA methylation.Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, Fraser HBGenome Res
Atypia of Undetermined Significance and Follicular Lesions of Undetermined Significance: Sonographic Assessment for Prediction of the Final Diagnosis.
J Ultrasound Med. 2015 May;34(5):767-774
Authors: Kamaya A, Lewis GH, Liu Y, Akatsu H, Kong C, Desser TS
OBJECTIVES: To determine whether radiologic assessment of thyroid nodules can potentially help guide clinical management after a cytologic diagnosis of atypia of undetermined significance or a follicular lesion of undetermined significance.
METHODS: We identified 41 patients with 41 thyroid nodules initially diagnosed as atypia or follicular lesions of undetermined significance on fine-needle aspiration that were subsequently definitively diagnosed by either surgical resection or repeated fine-needle aspiration. All sonograms of nodules were reviewed by 2 blinded board-certifiedradiologists. Lesions were assessed in 3 ways: (1) Mayo pattern classification as benign, indeterminate, or worrisome for malignancy (Ultrasound Q 2005; 21:157-165); (2) thyroid imaging reporting and data system scores (scale of 1-5) based on 2 different previously published scoring criteria (Park et al [Thyroid 2009; 19:1257-1264] and Kwak et al [Radiology 2011; 260:892-899]); and (3) binary classification as benign or malignant.
RESULTS: Of the 41 nodules, 25 had benign histologic findings, and 16 were malignant. Mayo pattern classification was 100% accurate for the benign score. Lesions with a Mayo score of indeterminate were malignant in 21% of cases (6 of 28) and benign in 79% (22 of 28). Lesions with a Mayo score of malignant were malignant in 91% of cases (10 of 11) and benign in 9% (1 of 11). Thyroid imaging reporting and data system scores had area under the receiver operating characteristic curve values of 0.827 for Park scores and 0.822 for Kwak scores. Radiologist binary classification of thyroid nodules showed 88% overall accuracy.
CONCLUSIONS: Radiologist assessment of thyroid nodules in cases of atypia of undetermined significance or follicular lesions of undetermined significance is highly predictive of the final diagnosis and can help guide management of thyroid nodules of these pathologic types.
PMID: 25911708 [PubMed - as supplied by publisher]
Solving the puzzle of human warfare requires an explanation of battle raids and cultural institutions.
Proc Natl Acad Sci U S A. 2015 Apr 24;
Authors: Zefferman MR, Baldini R, Mathew S
PMID: 25911638 [PubMed - as supplied by publisher]
Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.
FASEB J. 2015 Apr 24;
Authors: Lee J, Taylor SE, Smeriglio P, Lai J, Maloney WJ, Yang F, Bhutani N
Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early SRY (sex-determining region Y) box (Sox)9(low) cluster of differentiation (CD)44(low)CD140(low) prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9-regulated gene networks were identified in the Sox9(low) and Sox9(high) populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC-derived articular-like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular-like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening.-Lee, J., Taylor, S. E. B., Smeriglio, P., Lai, J., Maloney, W. J., Yang, F., Bhutani, N. Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells.
PMID: 25911615 [PubMed - as supplied by publisher]
Perioperative Management of Diabetic Patients Undergoing Hand Surgery.
J Hand Surg Am. 2015 May;40(5):1028-1031
Authors: Kang JR, Yao J
PMID: 25911211 [PubMed - as supplied by publisher]
Obsessional Disorders in al-Balkhi's 9th century treatise: Sustenance of the Body and Soul.
J Affect Disord. 2015 Mar 19;180:185-189
Authors: Awaad R, Ali S
Some argue that the earliest case of Obsessive-Compulsive Disorder (OCD) was reported by Robert Burton in his compendium The Anatomy of Melancholy (1621) and that only in the 19th century did modern concepts of OCD evolve, differentiating it from other types of mental illness. In this paper, we aim to reveal an even earlier presentation of the malady we now call OCD based on the 9th century work, Sustenance of the Body and Soul, written by Abu Zayd al-Balkhi during the Islamic Golden Era. Discovery of this manuscript reveals that Abu Zayd al-Balkhi should be credited with differentiating OCD from other forms of mental illnesses nearly a millennium earlier than is currently claimed by anthologies documenting the history of mental illness. Particular attention is paid to al-Balkhi's classifications, symptom descriptions, predisposing factors, and the treatment modalities for obsessional disorders. Analysis of this manuscript in light of the DSM-5 and modern scientific discoveries reveals transcultural diagnostic consistency of OCD across many centuries. Theoretical and clinical implications of these findings are also discussed.
PMID: 25911133 [PubMed - as supplied by publisher]
The MGMT promoter SNP rs16906252 is a risk factor for MGMT methylation in glioblastoma and is predictive of response to temozolomide.
Neuro Oncol. 2015 Apr 24;
Authors: Rapkins RW, Wang F, Nguyen HN, Cloughesy TF, Lai A, Ha W, Nowak AK, Hitchins MP, McDonald KL
BACKGROUND: Promoter methylation of O(6)-methylguanine-DNA methyltransferase (MGMT) is an important predictive biomarker in glioblastoma. The T variant of the MGMT promoter-enhancer single nucleotide polymorphism (SNP; rs16906252) has been associated with the presence of MGMT promoter methylation in other cancers. We examined the association of the T allele of rs16906252 with glioblastoma development, tumor MGMT methylation, MGMT protein expression, and survival outcomes.
METHODS: Two independent temozolomide-treated glioblastoma cohorts-one Australian (Australian Genomics and Clinical Outcomes of Glioma, n = 163) and the other American (University of California Los Angeles/Kaiser Permanente Los Angeles, n = 159)-were studied. Allelic bisulphite sequencing was used to determine if methylation was specific to the T allele. Additionally, we compared the incidence of the T allele between glioblastoma cases and matched controls to assess whether it was a risk factor for developing MGMT methylated glioblastoma.
RESULTS: Carriage of the T allele of the rs16906252 SNP was associated with both MGMT methylation and low MGMT protein expression and predicted significantly longer survival in temozolomide-treated patients with both MGMT methylated and nonmethylated glioblastoma. Methylation was linked to the T allele, inferring that the T variant plays a key role in the acquisition of MGMT methylation. Carriage of the T allele was associated with a significantly elevated risk of developing glioblastoma (adjusted odds ratio, 1.96; P = .013), increasing further when glioblastoma was classified by the presence of MGMT methylation (adjusted odds ratio, 2.86; P = .001).
CONCLUSIONS: The T allele of the rs16906252 SNP is a key determinant in the acquisition of MGMT methylation in glioblastoma. Temozolomide-treated patients with the rs16906252 T genotype have better survival, irrespective of tumor methylation status.
PMID: 25910840 [PubMed - as supplied by publisher]
Preparing to take the USMLE Step 1: a survey on medical students' self-reported study habits.
Postgrad Med J. 2015 Apr 24;
Authors: Kumar AD, Shah MK, Maley JH, Evron J, Gyftopoulos A, Miller C
BACKGROUND: The USA Medical Licensing Examination Step 1 is a computerised multiple-choice examination that tests the basic biomedical sciences. It is administered after the second year in a traditional four-year MD programme. Most Step 1 scores fall between 140 and 260, with a mean (SD) of 227 (22). Step 1 scores are an important selection criterion for residency choice. Little is known about which study habits are associated with a higher score.
OBJECTIVE: To identify which self-reported study habits correlate with a higher Step 1 score.
METHODS: A survey regarding Step 1 study habits was sent to third year medical students at Tulane University School of Medicine every year between 2009 and 2011. The survey was sent approximately 3 months after the examination.
RESULTS: 256 out of 475 students (54%) responded. The mean (SD) Step 1 score was 229.5 (22.1). Students who estimated studying more than 8-11 h per day had higher scores (p<0.05), but there was no added benefit with additional study time. Those who reported studying <40 days achieved higher scores (p<0.05). Those who estimated completing >2000 practice questions also obtained higher scores (p<0.01). Students who reported studying in a group, spending the majority of study time on practice questions or taking >40 preparation days did not achieve higher scores.
CONCLUSIONS: Certain self-reported study habits may correlate with a higher Step 1 score compared with others. Given the importance of achieving a high Step 1 score on residency choice, it is important to further identify which characteristics may lead to a higher score.
PMID: 25910497 [PubMed - as supplied by publisher]
A pooling-based approach to mapping genetic variants associated with DNA methylation.
Genome Res. 2015 Apr 24;
Authors: Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, Fraser HB
DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover less than 2% of the genome and cannot account for allele-specific methylation (ASM). Other studies have performed whole-genome bisulfite sequencing on a few individuals, but these lack statistical power to identify variants associated with DNA methylation. We present a novel approach in which bisulfite-treated DNA from many individuals is sequenced together in a single pool, resulting in a truly genome-wide map of DNA methylation. Compared to methods that do not account for ASM, our approach increases statistical power to detect associations while sharply reducing cost, effort, and experimental variability. As a proof of concept, we generated deep sequencing data from a pool of 60 human cell lines; we evaluated almost twice as many CpGs as the largest microarray studies and identified over 2,000 genetic variants associated with DNA methylation. We found that these variants are highly enriched for associations with chromatin accessibility and CTCF binding but are less likely to be associated with traits indirectly linked to DNA, such as gene expression and disease phenotypes. In summary, our approach allows genome-wide mapping of genetic variants associated with DNA methylation in any tissue of any species, without the need for individual-level genotype or methylation data.
PMID: 25910490 [PubMed - as supplied by publisher]
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