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Article ; Online: A two-stage design with two co-primary endpoints.

Song, James X

Contemporary clinical trials communications

2015 Volume 1, Page(s) 2–4

Abstract: Two-stage designs are commonly used in phase II oncology trial to mitigate the risk of exposing patients to an inefficacious drug. Typically, the decision of moving into stage 2 enrollment is made based on response rate in stage 1 patients; and trials ... ...

Abstract	Two-stage designs are commonly used in phase II oncology trial to mitigate the risk of exposing patients to an inefficacious drug. Typically, the decision of moving into stage 2 enrollment is made based on response rate in stage 1 patients; and trials are designed in the hypothesis testing framework. When the primary objective of a trial involves more than one efficacy endpoints it is desirable to extend the two-stage design to a setting that accommodates two hypotheses while controlling overall type I and II errors (α and β). In this manuscript, we propose a simple method of searching stopping boundaries of both hypotheses simultaneously that satisfy α and β constrains using binomial distribution. Several design characteristics of these selected boundaries are further examined in order to choose the most desirable design based on an objective function. Simulation is used to confirm the results. A trial design in metastatic breast cancer where both response rate and health-related quality of life are of interest is used as an example of the application of the proposed method. In conclusion, the proposed design is an extension of Simon Two-Stage Design. It can be applied to phase II oncology trials with two independent co-primary efficacy endpoints.
Language	English
Publishing date	2015-10-01
Publishing country	Netherlands
Document type	Journal Article
ISSN	2451-8654
ISSN (online)	2451-8654
DOI	10.1016/j.conctc.2015.08.002
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Article: Green Plant Protection Innovation: Challenges and Perspectives.

Song, Baoan / Seiber, James N / Duke, Stephen O / Li, Qing X

Engineering (Beijing, China)

2020 Volume 6, Issue 5, Page(s) 483–484

Keywords	covid19
Language	English
Publishing date	2020-04-15
Publishing country	China
Document type	Editorial
ZDB-ID	2886869-9
ISSN	2095-8099
ISSN	2095-8099
DOI	10.1016/j.eng.2020.04.001
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Article ; Online: Cobalt-Catalyzed Enantioselective Hydrogenation of Diaryl Ketones with Ferrocene-Based Secondary Phosphine Oxide Ligands.

Zeng, Liyao / Zhao, Menglong / Lin, Bijin / Song, Jingyuan / Tucker, James H R / Wen, Jialin / Zhang, Xumu

Organic letters

2023 Volume 25, Issue 33, Page(s) 6228–6233

Abstract: ... bidentate coordination pattern with cobalt was confirmed by an X-ray diffraction study. The bichelating ...

Abstract	A new class of cobalt catalytic system for asymmetric hydrogenation of ketones was herein reported, involving the development of novel ferrocene-based secondary phosphine oxide ligands. An unusual P-O bidentate coordination pattern with cobalt was confirmed by an X-ray diffraction study. The bichelating tetrahedral cobalt(II) complexes afforded high reactivities (up to 99% yield) and good to excellent enantioselectivities (up to 92% ee) in the AH of various
Language	English
Publishing date	2023-08-16
Publishing country	United States
Document type	Journal Article
ISSN	1523-7052
ISSN (online)	1523-7052
DOI	10.1021/acs.orglett.3c02530
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Article ; Online: A two-stage patient enrichment adaptive design in phase II oncology trials.

Song, James X

Contemporary clinical trials

2014 Volume 37, Issue 1, Page(s) 148–154

Abstract: Illustrated is the use of a patient enrichment adaptive design in a randomized phase II trial which allows the evaluation of treatment benefits by the biomarker expression level and makes interim adjustment according to the pre-specified rules. The ... ...

Abstract	Illustrated is the use of a patient enrichment adaptive design in a randomized phase II trial which allows the evaluation of treatment benefits by the biomarker expression level and makes interim adjustment according to the pre-specified rules. The design was applied to an actual phase II metastatic hepatocellular carcinoma (HCC) trial in which progression-free survival (PFS) in two biomarker-defined populations is evaluated at both interim and final analyses. As an extension, a short-term biomarker is used to predict the long-term PFS in a Bayesian model in order to improve the precision of hazard ratio (HR) estimate at the interim analysis. The characteristics of the extended design are examined in a number of scenarios via simulations. The recommended adaptive design is shown to be useful in a phase II setting. When a short-term maker which correlates with the long-term PFS is available, the design can be applied in smaller early phase trials in which PFS requires longer follow-up. In summary, the adaptive design offers flexibility in randomized phase II patient enrichment trials and should be considered in an overall personalized healthcare (PHC) strategy.
MeSH term(s)	Bayes Theorem ; Biomarkers, Tumor/metabolism ; Carcinoma, Hepatocellular/drug therapy ; Carcinoma, Hepatocellular/metabolism ; Disease-Free Survival ; Humans ; Liver Neoplasms/drug therapy ; Liver Neoplasms/metabolism ; Models, Statistical ; Proportional Hazards Models ; Research Design ; Treatment Outcome
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2014-01
Publishing country	United States
Document type	Clinical Trial, Phase II ; Journal Article ; Randomized Controlled Trial
ZDB-ID	2182176-8
ISSN	1559-2030 ; 1551-7144
ISSN (online)	1559-2030
ISSN	1551-7144
DOI	10.1016/j.cct.2013.12.001
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Zs.A 1581: Show issues

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Article ; Online: A multi-channel deep convolutional neural network for multi-classifying thyroid diseases.

Zhang, Xinyu / Lee, Vincent C S / Rong, Jia / Lee, James C / Song, Jiangning / Liu, Feng

Computers in biology and medicine

2022 Volume 148, Page(s) 105961

Abstract: Background and objective: Thyroid disease instances have been continuously increasing since the 1990s, and thyroid cancer has become the most rapidly rising disease among all the malignancies in recent years. Most existing studies focused on applying ... ...

Abstract	Background and objective: Thyroid disease instances have been continuously increasing since the 1990s, and thyroid cancer has become the most rapidly rising disease among all the malignancies in recent years. Most existing studies focused on applying deep convolutional neural networks for detecting thyroid cancer. Despite their satisfactory performance on binary classification tasks, limited studies have explored multi-class classification of thyroid disease types; much less is known of the diagnosis of co-existence situation for different types of thyroid diseases. Method: This study proposed a novel multi-channel convolutional neural network (CNN) architecture to address the multi-class classification task of thyroid disease. The multi-channel CNN merits from computed tomography characteristics to drive a comprehensive diagnostic decision for the overall thyroid gland, emphasizing the disease co-existence circumstance. Moreover, this study also examined alternative strategies to enhance the diagnostic accuracy of CNN models through concatenation of different scales of feature maps. Results: Benchmarking experiments demonstrate the improved performance of the proposed multi-channel CNN architecture compared with the standard single-channel CNN architecture. More specifically, the multi-channel CNN achieved an accuracy of 0.909±0.048, precision of 0.944±0.062, recall of 0.896±0.047, specificity of 0.994±0.001, and F1 of 0.917±0.057, in contrast to the single-channel CNN, which obtained 0.902±0.004, 0.892±0.005, 0.909±0.002, 0.993±0.001, 0.898±0.003, respectively. In addition, the proposed model was evaluated in different gender groups; it reached a diagnostic accuracy of 0.908 for the female group and 0.901 for the male group. Conclusion: Collectively, the results highlight that the proposed multi-channel CNN has excellent generalization and has the potential to be deployed to provide computational decision support in clinical settings.
MeSH term(s)	Female ; Humans ; Male ; Neural Networks, Computer ; Thyroid Diseases ; Thyroid Neoplasms ; Tomography, X-Ray Computed
Language	English
Publishing date	2022-08-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105961
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Zs.A 653: Show issues

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Article ; Online: A two-stage design with two co-primary endpoints

James X. Song

Contemporary Clinical Trials Communications, Vol 1, Iss C, Pp 2-

2015 Volume 4

Abstract	Two-stage designs are commonly used in phase II oncology trial to mitigate the risk of exposing patients to an inefficacious drug. Typically, the decision of moving into stage 2 enrollment is made based on response rate in stage 1 patients; and trials are designed in the hypothesis testing framework. When the primary objective of a trial involves more than one efficacy endpoints it is desirable to extend the two-stage design to a setting that accommodates two hypotheses while controlling overall type I and II errors (α and β). In this manuscript, we propose a simple method of searching stopping boundaries of both hypotheses simultaneously that satisfy α and β constrains using binomial distribution. Several design characteristics of these selected boundaries are further examined in order to choose the most desirable design based on an objective function. Simulation is used to confirm the results. A trial design in metastatic breast cancer where both response rate and health-related quality of life are of interest is used as an example of the application of the proposed method. In conclusion, the proposed design is an extension of Simon Two-Stage Design. It can be applied to phase II oncology trials with two independent co-primary efficacy endpoints.
Keywords	Phase II oncology trials ; Co-primary endpoints ; Two-stage design ; Medicine (General) ; R5-920
Subject code	310
Language	English
Publishing date	2015-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparison of setup accuracy of optical surface image versus orthogonal x-ray images for VMAT of the left breast using deep-inspiration breath-hold.

Lu, Wei / Hong, Linda X / Yamada, Nelson / Berry, Sean L / Song, Yulin / Choi, Wookjin / Cerviño, Laura I / Tang, Xiaoli / Mechalakos, James G / Romesser, Paul B / Powell, Simon / Li, Guang

Journal of applied clinical medical physics

2023 Volume 24, Issue 12, Page(s) e14117

Abstract: To compare the setup accuracy of optical surface image (OSI) versus orthogonal x-ray images (2DkV ...

Abstract	To compare the setup accuracy of optical surface image (OSI) versus orthogonal x-ray images (2DkV) using cone beam computed tomography (CBCT) as ground truth for radiotherapy of left breast cancer in deep-inspiration breath-hold (DIBH). Ten left breast DIBH patients treated with volumetric modulated arc therapy (VMAT) were studied retrospectively. OSI, 2DkV, and CBCT were acquired weekly at treatment setup. OSI, 2DkV, and CBCT were registered to planning CT or planning DRR based on a breast surface region of interest (ROI), bony anatomy (chestwall and sternum), and both bony anatomy and breast surface, respectively. These registrations provided couch shifts for each imaging system. The setup errors, or the difference in couch shifts between OSI and CBCT were compared to those between 2DkV and CBCT. A second OSI was acquired during last beam delivery to evaluate intrafraction motion. The median absolute setup errors were (0.21, 0.27, 0.23 cm, 0.6°, 1.3°, 1.0°) for OSI, and (0.26, 0.24, 0.18 cm, 0.9°, 1.0°, 0.6°) for 2DkV in vertical, longitudinal and lateral translations, and in rotation, roll and pitch, respectively. None of the setup errors was significantly different between OSI and 2DkV. For both systems, the systematic and random setup errors were ≤0.6 cm and ≤1.5° in all directions. Nevertheless, larger setup errors were observed in some sessions in both systems. There was no correlation between OSI and CBCT whereas there was modest correlation between 2DkV and CBCT. The intrafraction motion in DIBH detected by OSI was small with median absolute translations <0.2 cm, and rotations ≤0.4°. Though OSI showed comparable and small setup errors as 2DkV, it showed no correlation with CBCT. We concluded that to achieve accurate setup for both bony anatomy and breast surface, daily 2DkV can't be omitted following OSI for left breast patients treated with DIBH VMAT.
MeSH term(s)	Humans ; Female ; Radiotherapy, Intensity-Modulated ; Retrospective Studies ; X-Rays ; Cone-Beam Computed Tomography/methods ; Breast Neoplasms/diagnostic imaging ; Breast Neoplasms/radiotherapy ; Radiotherapy Planning, Computer-Assisted/methods ; Breath Holding
Language	English
Publishing date	2023-08-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010347-5
ISSN	1526-9914 ; 1526-9914
ISSN (online)	1526-9914
ISSN	1526-9914
DOI	10.1002/acm2.14117
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Article ; Online: Effects of heterozygous deletion of autism-related gene Cullin-3 in mice.

Xia, Qiang-Qiang / Walker, Angela K / Song, Chenghui / Wang, Jing / Singh, Anju / Mobley, James A / Xuan, Zhong X / Singer, Jeffrey D / Powell, Craig M

PloS one

2023 Volume 18, Issue 7, Page(s) e0283299

Abstract: Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating ... ...

Abstract	Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In area CA1 of hippocampus, reduction of Cul3 significantly increased mEPSC frequency but not amplitude nor baseline evoked synaptic transmission or paired-pulse ratio. Sholl and spine analysis data suggest there is a small yet significant difference in CA1 pyramidal neuron dendritic branching and stubby spine density. Unbiased proteomic analysis of Cul3 heterozygous brain tissue revealed dysregulation of various cytoskeletal organization proteins, among others. Overall, our results suggest that Cul3 heterozygous deletion impairs spatial object recognition memory, alters cytoskeletal organization proteins, but does not cause major hippocampal neuronal morphology, functional, or behavioral abnormalities in adult global Cul3 heterozygous mice.
MeSH term(s)	Animals ; Mice ; Autism Spectrum Disorder/genetics ; Autistic Disorder/genetics ; Cullin Proteins/genetics ; Cullin Proteins/metabolism ; Protein Binding ; Proteomics
Chemical Substances	Cullin Proteins ; Cul3 protein, mouse
Language	English
Publishing date	2023-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0283299
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Article ; Online: The impact of marital status on tumor aggressiveness, treatment, and screening among black and white men diagnosed with prostate cancer.

Khan, Saira / Fuzzell, Lindsay / Langston, Marvin / Han, Yunan / Moore, Justin X / Gilbert, Keon / Sutcliffe, Siobhan / Bensen, Jeannette T / Mohler, James L / Fontham, Elizabeth T H / Song, Lixin / Lewis-Thames, Marquita W

Cancer causes & control : CCC

2023 Volume 35, Issue 3, Page(s) 531–539

Abstract: Purpose: To examine the association of marital status with prostate cancer outcomes in a racially-diverse cohort.: Methods: The study population consisted of men (1010 Black; 1070 White) with incident prostate cancer from the baseline North Carolina- ... ...

Abstract	Purpose: To examine the association of marital status with prostate cancer outcomes in a racially-diverse cohort. Methods: The study population consisted of men (1010 Black; 1070 White) with incident prostate cancer from the baseline North Carolina-Louisiana Prostate Cancer (PCaP) cohort. Marital status at time of diagnosis and screening history were determined by self-report. The binary measure of marital status was defined as married (including living as married) vs. not married (never married, divorced/separated, or widowed). High-aggressive tumors were defined using a composite measure of PSA, Gleason Score, and stage. Definitive treatment was defined as receipt of radical prostatectomy or radiation. Multivariable logistic regression was used to examine the association of marital status with (1) high-aggressive tumors, (2) receipt of definitive treatment, and (3) screening history among Black and White men with prostate cancer. Results: Black men were less likely to be married than White men (68.1% vs. 83.6%). Not being married (vs. married) was associated with increased odds of high-aggressive tumors in the overall study population (adjusted Odds Ratio (aOR): 1.56; 95% Confidence Interval (CI): 1.20-2.02) and both Black and White men in race-stratified analyses. Unmarried men were less likely to receive definitive treatment in the overall study population (aOR: 0.68; 95% CI: 0.54-0.85). In race-stratified analyses, unmarried Black men were less likely to receive definitive treatment. Both unmarried Black and White men were less likely to have a history of prostate cancer screening than married men. Conclusion: Lower rates of marriage among Black men might signal decreased support for treatment decision-making, symptom management, and caregiver support which could potentially contribute to prostate cancer disparities.
MeSH term(s)	Male ; Humans ; Prostatic Neoplasms/pathology ; Early Detection of Cancer ; Prostate-Specific Antigen ; White ; Marital Status
Chemical Substances	Prostate-Specific Antigen (EC 3.4.21.77)
Language	English
Publishing date	2023-11-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1064022-8
ISSN	1573-7225 ; 0957-5243
ISSN (online)	1573-7225
ISSN	0957-5243
DOI	10.1007/s10552-023-01821-9
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Zs.A 3375: Show issues

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Article ; Online: Alteration of endothelial permeability ensures cardiomyocyte survival from ischemic insult in the subendocardium of the heart.

Chu, Qing / Song, Xin / Xiao, Ying / Kang, Y James

Experimental biology and medicine (Maywood, N.J.)

2023 Volume 248, Issue 16, Page(s) 1364–1372

Abstract: Previous studies have shown that cardiomyocytes in the subendocardial region of myocardium survive from ischemic insult. This study was undertaken to explore possible mechanisms for the survival of these cardiomyocytes, focusing on changes in endothelial ...

Abstract	Previous studies have shown that cardiomyocytes in the subendocardial region of myocardium survive from ischemic insult. This study was undertaken to explore possible mechanisms for the survival of these cardiomyocytes, focusing on changes in endothelial cells (ECs) and blood supply. C57/B6 mice were subjected to permanent ligation of left anterior descending (LAD) coronary artery to induce myocardial ischemia (MI). The hearts were harvested at 1, 4, and 7 days post MI and examined for histological changes. It was found that the survival of cardiomyocytes was associated with a preservation of ECs in the subendocardial region, as revealed by EC-specific
MeSH term(s)	Mice ; Animals ; Myocytes, Cardiac/metabolism ; Endothelial Cells/metabolism ; Myocardium/metabolism ; Myocardial Ischemia/metabolism
Language	English
Publishing date	2023-10-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	4015-0
ISSN	1535-3699 ; 1525-1373 ; 0037-9727
ISSN (online)	1535-3699 ; 1525-1373
ISSN	0037-9727
DOI	10.1177/15353702231194344
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