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Article ; Online: Preface.

Curtis, Christina / Chin, Lynda

Biochimica et biophysica acta. Reviews on cancer

2021 Volume 1876, Issue 2, Page(s) 188617

MeSH term(s)	Artificial Intelligence ; Humans ; Machine Learning ; Neoplasms
Language	English
Publishing date	2021-08-20
Publishing country	Netherlands
Document type	Editorial ; Introductory Journal Article
ZDB-ID	2918802-7
ISSN	1879-2561 ; 0304-419X
ISSN (online)	1879-2561
ISSN	0304-419X
DOI	10.1016/j.bbcan.2021.188617
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Article ; Online: A digital highway for data fluidity and data equity in precision medicine.

Chin, Lynda / Khozin, Sean

Biochimica et biophysica acta. Reviews on cancer

2021 Volume 1876, Issue 1, Page(s) 188575

Abstract: Recent technological advances continue to expand the universe of big data in biomedicine along the four axes of variety, veracity, volume, and velocity, fueling innovations in research and discovery while transforming care delivery. These advances allow ... ...

Abstract	Recent technological advances continue to expand the universe of big data in biomedicine along the four axes of variety, veracity, volume, and velocity, fueling innovations in research and discovery while transforming care delivery. These advances allow quantitative capture of multimodal health, behavioral, social, and environmental data from n-of-all in near real-time to support the development of new therapies and personalization of treatment decisions for the n-of-one. Application of advanced analytical methods, including artificial intelligence and machine learning, to these modern data assets can greatly propel our understanding of health and disease, accelerating the development of safer and more effective anticancer therapies. In this perspective, we rationalize the creation of a universally accessible digital highway system as a foundational infrastructure to enable data fluidity in an equitable manner. An interoperable and integrated digital inter-state highway can facilitate efficient derivation of insights from biomedical big data to improve health outcomes and ensure that the U.S. remains at the leading-edge innovations in technology, advanced analytics, and precision medicine.
Language	English
Publishing date	2021-05-29
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2918802-7
ISSN	1879-2561 ; 0304-419X
ISSN (online)	1879-2561
ISSN	0304-419X
DOI	10.1016/j.bbcan.2021.188575
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Article ; Online: The Impact of the Older Person's Grant Expansion on Hypertension Among Older Men in Rural South Africa: Findings From the HAALSI Cohort.

Chang, Haeyoon / Jock, Janet / Rosenberg, Molly S / Li, Chihua / Cho, Tsai-Chin / Gaziano, Thomas A / Lisabeth, Lynda / Kobayashi, Lindsay C

Innovation in aging

2024 Volume 8, Issue 4, Page(s) igae010

Abstract: Background and objectives: Hypertension is a major modifiable contributor to disease burden in sub-Saharan Africa. We exploited an expansion to age eligibility for men in South Africa's noncontributory public pension to assess the impact of pension ... ...

Abstract	Background and objectives: Hypertension is a major modifiable contributor to disease burden in sub-Saharan Africa. We exploited an expansion to age eligibility for men in South Africa's noncontributory public pension to assess the impact of pension eligibility on hypertension in a rural, low-income South African setting. Research design and methods: Data were from 1 247 men aged ≥60 in the population-representative Health and Aging in Africa: A Longitudinal Study of an INDEPTH Community in South Africa in 2014/2015. We identified cohorts of men from 0 (controls, aged ≥65 at pension expansion) through 5 years of additional pension eligibility based on their birth year. Using the modified Framingham Heart Study hypertension risk prediction model, and the Wand et al. model modified for the South African population, we estimated the difference in the probabilities of hypertension for men who benefitted from the pension expansion relative to the control. We conducted a negative control analysis among older women, who were not eligible for pension expansion, to assess the robustness of our findings. Results: Older men with 5 additional years of pension eligibility had a 6.9-8.1 percentage point greater probability of hypertension than expected without the pension expansion eligibility. After accounting for birth cohort effects through a negative control analysis involving older women reduced estimates to a 3.0-5.2 percentage point greater probability of hypertension than expected. We observed a mean 0.2 percentage point increase in the probability of hypertension per additional year of pension eligibility, but this trend was not statistically significant. Discussion and implications: Although the Older Person's Grant is important for improving the financial circumstances of older adults and their families in South Africa, expanded pension eligibility may have a small, negative short-term effect on hypertension among older men in this rural, South African setting.
Language	English
Publishing date	2024-02-08
Publishing country	England
Document type	Journal Article
ISSN	2399-5300
ISSN (online)	2399-5300
DOI	10.1093/geroni/igae010
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Article ; Online: Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.

Akdemir, Kadir C / Le, Victoria T / Chandran, Sahaana / Li, Yilong / Verhaak, Roel G / Beroukhim, Rameen / Campbell, Peter J / Chin, Lynda / Dixon, Jesse R / Futreal, P Andrew

Nature genetics

2023 Volume 55, Issue 6, Page(s) 1079

Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Published Erratum
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/s41588-023-01318-w
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Zs.A 3613: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Genome engineering - Matching supply with demand.

Gutschner, Tony / Chin, Lynda

Cell cycle (Georgetown, Tex.)

2016 Volume 15, Issue 11, Page(s) 1395–1396

MeSH term(s)	CRISPR-Cas Systems ; Genetic Engineering ; Genome
Language	English
Publishing date	2016-04-06
Publishing country	United States
Document type	Editorial
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.1080/15384101.2016.1171647
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Article ; Online: A Study Design to Harmonize Patient-Reported Outcomes Across Data Sets.

McKelvey, Brittany A / Berk, Alexandra / Chin, Lynda / Hudgens, Stacie / Kudel, Ian / O'Hagan, Ronan C / Patel, Amila / Scott, Julie / Stires, Hillary / Wang, Sam / Wujcik, Debra / Stewart, Mark / Allen, Jeff

JCO clinical cancer informatics

2023 Volume 7, Page(s) e2200161

Abstract: Purpose: Using patient-reported outcomes (PROs) provides important insights from the patient's perspective and can be valuable to monitor and manage treatment-related adverse events during cancer treatment. Additionally, the digital administration of ... ...

Abstract	Purpose: Using patient-reported outcomes (PROs) provides important insights from the patient's perspective and can be valuable to monitor and manage treatment-related adverse events during cancer treatment. Additionally, the digital administration of PROs (electronic PROs [ePROs]) provides real-time updates to clinical care teams on treatment-related symptoms in-between clinic visits. However, given the variability in the methodology and timing of the data collection, using and harmonizing these data across different systems remains challenging. Identifying data elements to capture and operating procedures for harmonization across ePRO tools will expedite efforts to generate relevant and robust data on use of ePRO data in clinical care. Methods: Friends of Cancer Research assembled a consortium of project partners from key health care sectors to align on a framework for ePRO data capture across ePRO tools and assessment of the impact of ePRO data capture on patient outcomes. Results: We identified challenges and opportunities to align ePRO data capture across ePRO tools and aligned on key data elements for assessing the impact of ePRO data capture on patient care and outcomes. Ultimately, we proposed a study protocol to leverage ePRO data for symptom and adverse event management to measure real-world effectiveness of ePRO tool implementation on patient care and outcomes. Conclusion: This work provides considerations for harmonizing ePRO data sets and a common framework to align across multiple ePRO tools to assess the value of ePROs for improving patient outcomes. Future efforts to interpret evidence and evaluate the impact of ePRO tools on patient outcomes will be aided by improved alignment across studies.
MeSH term(s)	Humans ; Patient Reported Outcome Measures ; Software ; Data Collection ; Patient Care ; Research Design
Language	English
Publishing date	2023-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2473-4276
ISSN (online)	2473-4276
DOI	10.1200/CCI.22.00161
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Article ; Online: HiCPlotter integrates genomic data with interaction matrices.

Akdemir, Kadir Caner / Chin, Lynda

Genome biology

2015 Volume 16, Page(s) 198

Abstract: Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or ... ...

Abstract	Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or the presence of architectural proteins have been implicated in regulation and assembly of the chromatin architecture. Therefore, comprehensive visualization of this multi-faceted structure is important to unravel the connections between nuclear architecture and transcriptional regulation. Here, we present an easy-to-use open-source visualization tool, HiCPlotter, to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. https://github.com/kcakdemir/HiCPlotter.
MeSH term(s)	Animals ; Chromatin/genetics ; DNA Replication/genetics ; Data Mining/methods ; Gene Expression Regulation ; Genome/genetics ; Software
Chemical Substances	Chromatin
Language	English
Publishing date	2015-09-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/s13059-015-0767-1
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Article ; Online: Quantifying Patient-Initiated Upper Extremity Movement After Surgical Reconstruction for Adult Pan-Brachial Plexus Injury.

Muhlestein, Whitney E / Chang, Tommy Nai-Jen / Chang, Kate W-C / Lu, Johnny Chuieng-Yi / Chen, Pei-Ju / Chung, Kevin C / Yang, Lynda J-S / Brown, Susan H / Chuang, David Chwei-Chin

Neurosurgery

2023 Volume 94, Issue 3, Page(s) 552–558

Abstract: Background and objectives: Determining functional recovery in adult patients with traumatic pan-brachial plexus injury (pBPI) is hampered by the fact that most outcome measures are collected in the clinical setting and may not reflect arm use in the ... ...

Abstract	Background and objectives: Determining functional recovery in adult patients with traumatic pan-brachial plexus injury (pBPI) is hampered by the fact that most outcome measures are collected in the clinical setting and may not reflect arm use in the real world. This study's objectives were to demonstrate the feasibility of using wearable motion sensor technology to quantify spontaneous arm movement in adult patients with pBPI after surgical reconstruction and report the time and intensity with which the affected arm was used. Methods: Twenty-nine patients with pBPI who underwent surgical reconstruction at least 2 years prior were included in this study. Study participants wore an accelerometer on bilateral arms for 7 days. The vector time (VT) and magnitude with which each arm moved were collected and divided by the same values collected from the uninjured arm to generate a ratio (VT and vector magnitude [VM], respectively) to quantify differences between the arms. Correlations between VT, VM, and patient demographic and physician-elicited clinical measures were calculated. Patients were enrolled at Chang Gung Memorial Hospital, Linkou Medical Center, Taiwan, and data analysis was performed at the University of Michigan. Results: Twelve patients had pan-avulsion injuries, and 17 patients had C5 rupture with C6-T1 avulsion injuries. All underwent nerve reconstruction with contralateral C7 or ipsilateral C5 nerve roots as donors. At mean 7.3 years after surgery, the mean VT ratio was 0.54 ± 0.13 and the mean VM ratio was 0.30 ± 0.13. Both VT and VM ratios were significantly correlated with patient employment and movements at the elbow and forearm. Conclusion: Wearable motion detection technology can capture spontaneous, real-world movements of the arm in patients who have undergone surgical reconstruction for pBPI. Despite severe injuries, these patients are able to use their affected arm 50% of the time and with 30% of the intensity of their unaffected arm, which is positively correlated with return to work after injury. These data support the use of surgical reconstruction for pBPI.
MeSH term(s)	Adult ; Humans ; Brachial Plexus Neuropathies/surgery ; Nerve Transfer ; Brachial Plexus/surgery ; Brachial Plexus/injuries ; Upper Extremity/surgery ; Arm ; Treatment Outcome
Language	English
Publishing date	2023-09-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	135446-2
ISSN	1524-4040 ; 0148-396X
ISSN (online)	1524-4040
ISSN	0148-396X
DOI	10.1227/neu.0000000000002698
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Zs.A 1424: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Chromosome 10, frequently lost in human melanoma, encodes multiple tumor-suppressive functions.

Kwong, Lawrence N / Chin, Lynda

Cancer research

2014 Volume 74, Issue 6, Page(s) 1814–1821

Abstract: Although many DNA aberrations in melanoma have been well characterized, including focal amplification and deletions of oncogenes and tumor suppressors, broad regions of chromosomal gain and loss are less well understood. One possibility is that these ... ...

Abstract	Although many DNA aberrations in melanoma have been well characterized, including focal amplification and deletions of oncogenes and tumor suppressors, broad regions of chromosomal gain and loss are less well understood. One possibility is that these broad events are a consequence of collateral damage from targeting single loci. Another possibility is that the loss of large regions permits the simultaneous repression of multiple tumor suppressors by broadly decreasing the resident gene dosage and expression. Here, we test this hypothesis in a targeted fashion using RNA interference to suppress multiple candidate residents in broad regions of loss. We find that loss of chromosome regions 6q, 10, and 11q21-ter is correlated with broadly decreased expression of most resident genes and that multiple resident genes impacted by broad regional loss of chromosome 10 are tumor suppressors capable of affecting tumor growth and/or invasion. We also provide additional functional support for Ablim1 as a novel tumor suppressor. Our results support the hypothesis that multiple cancer genes are targeted by regional chromosome copy number aberrations.
MeSH term(s)	Animals ; Cell Line, Tumor ; Chromosome Deletion ; Chromosomes, Human, Pair 10/genetics ; DNA Copy Number Variations ; Gene Knockdown Techniques ; Genes, Tumor Suppressor ; Humans ; LIM Domain Proteins/genetics ; Lung Neoplasms/genetics ; Lung Neoplasms/metabolism ; Lung Neoplasms/secondary ; Melanoma, Experimental/genetics ; Melanoma, Experimental/metabolism ; Melanoma, Experimental/pathology ; Mice, Nude ; Microfilament Proteins/genetics ; Neoplasm Invasiveness ; Neoplasm Transplantation ; RNA, Small Interfering/genetics ; Transcriptome
Chemical Substances	ABLIM1 protein, human ; LIM Domain Proteins ; Microfilament Proteins ; RNA, Small Interfering
Language	English
Publishing date	2014-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1432-1
ISSN	1538-7445 ; 0008-5472
ISSN (online)	1538-7445
ISSN	0008-5472
DOI	10.1158/0008-5472.CAN-13-1446
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Article: HiCPlotter integrates genomic data with interaction matrices

Akdemir, Kadir Caner / Chin, Lynda

Genome biology. 2015 Dec., v. 16, no. 1

2015

Abstract	Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or the presence of architectural proteins have been implicated in regulation and assembly of the chromatin architecture. Therefore, comprehensive visualization of this multi-faceted structure is important to unravel the connections between nuclear architecture and transcriptional regulation. Here, we present an easy-to-use open-source visualization tool, HiCPlotter, to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. https://github.com/kcakdemir/HiCPlotter
Keywords	Animalia ; DNA replication ; chromatin ; non-coding RNA ; transcription (genetics)
Language	English
Dates of publication	2015-12
Size	p. 198.
Publishing place	BioMed Central
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/s13059-015-0767-1
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