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Book ; Online ; E-Book: Data science for infectious disease data analytics

Wang, Lily

an introduction with R

(Data science series)

2022

Author's details	Lily Wang
Series title	Data science series
Keywords	Electronic books
Language	English
Size	1 Online-Ressource (xxii, 397 Seiten), Illustrationen
Edition	First edition
Publisher	CRC Press LLC
Publishing place	Milton
Publishing country	United States
Document type	Book ; Online ; E-Book
Note	Description based on publisher supplied metadata and other sources
Remark	Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
HBZ-ID	HT021586019
ISBN	978-1-003-25632-8 ; 9781000643060 ; 9781032187426 ; 9781032188058 ; 1-003-25632-5 ; 1000643069 ; 1032187425 ; 1032188057
DOI	10.1201/9781003256328
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article: Response to comment on "Definite chemoradiotherapy for early-stagebulky cervical cancer".

Hsieh, He-Yuan / Lu, Chien-Hsing / Wang, Lily

Journal of the Formosan Medical Association = Taiwan yi zhi

2023 Volume 123, Issue 3, Page(s) 418–419

MeSH term(s)	Female ; Humans ; Uterine Cervical Neoplasms/radiotherapy ; Chemoradiotherapy
Language	English
Publishing date	2023-12-20
Publishing country	Singapore
Document type	Letter
ZDB-ID	2096659-3
ISSN	1876-0821 ; 0929-6646
ISSN (online)	1876-0821
ISSN	0929-6646
DOI	10.1016/j.jfma.2023.10.020
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Article ; Online: Speech and noise levels measured in occupied K-12 classrooms.

Wang, Lily M / Brill, Laura C

The Journal of the Acoustical Society of America

2021 Volume 150, Issue 2, Page(s) 864

Abstract: This project acquired sound levels logged across six school days and impulse responses in 220 classrooms across four K-12 grades. Seventy-four percent met reverberation time recommendations. Sound levels were processed to estimate occupied signal-to- ... ...

Abstract	This project acquired sound levels logged across six school days and impulse responses in 220 classrooms across four K-12 grades. Seventy-four percent met reverberation time recommendations. Sound levels were processed to estimate occupied signal-to-noise ratios (SNRs), using Gaussian mixture modeling and from daily equivalent and statistical levels. A third method, k-means clustering, estimated SNR more precisely, separating data on nine dimensions into one group with high levels across speech frequencies and one without. The SNRs calculated as the daily difference between the average levels for the speech and non-speech clusters are found to be lower than 15 dB in 27.3% of the classrooms and differ from using the other two methods. The k-means data additionally indicate that speech occurred 30.5%-81.2% of the day, with statistically larger percentages found in grade 3 compared to higher grades. Speech levels exceeded 65 dBA 35% of the day, and non-speech levels exceeded 50 dBA 32% of the day, on average, with grades 3 and 8 experiencing speech levels exceeding 65 dBA statistically more often than the other two grades. Finally, classroom speech and non-speech levels were significantly correlated, with a 0.29 dBA increase in speech levels for every 1 dBA in non-speech levels.
MeSH term(s)	Schools ; Signal-To-Noise Ratio ; Speech ; Speech Perception
Language	English
Publishing date	2021-09-02
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0005815
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Article: Long-term treatment outcomes/toxicities of definite chemoradiotherapy (intensity-modulated radiation therapy) for early-stage "bulky" cervical cancer and survival impact of histological subtype.

Hsieh, He-Yuan / Lu, Chien-Hsing / Wang, Lily

Journal of the Formosan Medical Association = Taiwan yi zhi

2022 Volume 122, Issue 3, Page(s) 221–229

Abstract: Background: To investigate the long-term treatment outcomes of early stage bulky cervical cancer treated with definite chemoradiotherapy (CCRT) using intensity-modulated radiotherapy (IMRT) followed by intracavity brachytherapy (ICRT) and the impact of ... ...

Abstract	Background: To investigate the long-term treatment outcomes of early stage bulky cervical cancer treated with definite chemoradiotherapy (CCRT) using intensity-modulated radiotherapy (IMRT) followed by intracavity brachytherapy (ICRT) and the impact of histologic subtype on survival. Methods: From 2004 to 2016, 126 patients with FIGO stage IB2-IIB bulky (≥4 cm) cervical cancer treated with CCRT followed by ICRT were retrospectively reviewed. Long-term treatment-related acute/late toxicities and treatment outcomes including overall survival (OS), locoregional recurrence-free survival (LRRFS), and distant metastasis-free survival (DMFS) were reported. Different histologic subtype between squamous cell carcinoma (SCC) and adenocarcinoma/adenosquamous carcinoma (AC/ASC)) of uterine cervix were also compared. Results: Median follow-up time for alive patients was 117 months. The 5-year OS, LRRFS and DMFS were 75.3%, 87.8% and 75.6%, respectively. The most common ≥ grade 3 acute toxicity was hematologic toxicity (41.3%). The rates of ≥ grade 3 late toxicities were 4% of proctitis, 0.8% of urethral stricture and 0.8% of radiation dermatitis (peri-anal skin necrosis and gangrene). The 5-year OS/LRRFS/DMFS for SCC and AC/ASC were 81.7%/93.7%/81.5% and 51.9%/65.8%/53.5%, respectively (all log-rank p < 0.05). The AC/ASC histology was an independent prognostic factor for worse OS, LRRFS, and DMFS (All p < 0.05). Conclusion: After long-term follow up, definite CCRT using IMRT followed by ICRT is a feasible treatment with favorable acute and late treatment toxicities for patients with early stage bulky cervical cancer. This treatment outcomes were excellent for "bulky" FIGO stage IB2-IIB SCC of the uterine cervix but seemed insufficient for AC/ASC of uterine cervix.
MeSH term(s)	Female ; Humans ; Uterine Cervical Neoplasms/pathology ; Radiotherapy, Intensity-Modulated ; Retrospective Studies ; Neoplasm Staging ; Treatment Outcome ; Carcinoma, Squamous Cell/pathology ; Carcinoma, Adenosquamous/pathology ; Chemoradiotherapy ; Adenocarcinoma/pathology
Language	English
Publishing date	2022-11-12
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2096659-3
ISSN	1876-0821 ; 0929-6646
ISSN (online)	1876-0821
ISSN	0929-6646
DOI	10.1016/j.jfma.2022.10.012
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Article ; Online: Imaging Appearance of Migraine and Tension Type Headache.

Mahammedi, Abdelkader / Wang, Lily L / Vagal, Achala S

Neurologic clinics

2022 Volume 40, Issue 3, Page(s) 491–505

MeSH term(s)	Diagnostic Imaging ; Humans ; Migraine Disorders/diagnostic imaging ; Tension-Type Headache/diagnostic imaging
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1013148-6
ISSN	1557-9875 ; 0733-8619
ISSN (online)	1557-9875
ISSN	0733-8619
DOI	10.1016/j.ncl.2022.02.002
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Article ; Online: Imaging of Headache Attributed to Vascular Disorders.

Wang, Lily L / Mahammedi, Abdelkader / Vagal, Achala S

Neurologic clinics

2022 Volume 40, Issue 3, Page(s) 507–530

Abstract: Imaging is essential in the diagnosis of vascular causes of headaches. With advances in technology, there are increasing options of imaging modalities to choose from, each with its own advantages and disadvantages. This article will focus on imaging ... ...

Abstract	Imaging is essential in the diagnosis of vascular causes of headaches. With advances in technology, there are increasing options of imaging modalities to choose from, each with its own advantages and disadvantages. This article will focus on imaging pearls and pitfalls of vascular causes of headaches. These include aneurysms, vasculitides, vascular malformations, and cerebral venous thrombosis.
MeSH term(s)	Headache/diagnostic imaging ; Headache/etiology ; Humans ; Magnetic Resonance Angiography ; Tomography, X-Ray Computed
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1013148-6
ISSN	1557-9875 ; 0733-8619
ISSN (online)	1557-9875
ISSN	0733-8619
DOI	10.1016/j.ncl.2022.02.004
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Article ; Online: Investigating multidimensional characteristics of noise signals with tones from building mechanical systems and their effects on annoyance.

Lee, Joonhee / Wang, Lily M

The Journal of the Acoustical Society of America

2020 Volume 147, Issue 1, Page(s) 108

Abstract: This paper investigates multidimensional characteristics of tonal noise from heating, ventilation, and air-conditioning systems, besides loudness and tonality, to improve prediction of annoyance. Two studies were conducted: multidimensional scaling (MDS) ...

Abstract	This paper investigates multidimensional characteristics of tonal noise from heating, ventilation, and air-conditioning systems, besides loudness and tonality, to improve prediction of annoyance. Two studies were conducted: multidimensional scaling (MDS) analysis to determine what other perceptual signal characteristics are important and perceptual weight analysis (PWA) to understand the impact of multiple tones in a signal. In the MDS study, paired comparison tasks were conducted to gather similarity and annoyance data. Results show that the latent perceptual dimensions are related to the signal's tonality, loudness, sharpness, and roughness. Including metrics for these perceptions, except roughness, improves the performance of earlier annoyance prediction models. Including both sharpness and tonal audibility does not further improve prediction performance, though. In the PWA study, noise stimuli with five-tone complexes between 125 Hz and 2 kHz were generated for subjective testing to obtain a perceptual weighting function. The levels of each tone were randomly adjusted for every trial, and both harmonic and inharmonic tone complexes were utilized. The PWA result was applied as a spectral weighting function to calculate a proposed weighted-sum tonal audibility metric. Utilizing the proposed metric instead of the traditional tonal audibility metric improves annoyance prediction to a similar degree as including sharpness.
MeSH term(s)	Acoustic Stimulation ; Acoustics ; Adult ; Auditory Perception ; Female ; Humans ; Loudness Perception ; Male ; Noise ; Psychoacoustics ; Signal Processing, Computer-Assisted ; Young Adult
Language	English
Publishing date	2020-01-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	219231-7
ISSN	1520-8524 ; 0001-4966
ISSN (online)	1520-8524
ISSN	0001-4966
DOI	10.1121/10.0000487
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Article: Transcriptome Meta-Analysis of Triple-Negative Breast Cancer Response to Neoadjuvant Chemotherapy.

Zhang, Wei / Li, Emma / Wang, Lily / Lehmann, Brian D / Chen, X Steven

Cancers

2023 Volume 15, Issue 8

Abstract: Triple-negative breast cancer (TNBC) is a heterogeneous disease with varying responses to neoadjuvant chemotherapy (NAC). The identification of biomarkers to predict NAC response and inform personalized treatment strategies is essential. In this study, ... ...

Abstract	Triple-negative breast cancer (TNBC) is a heterogeneous disease with varying responses to neoadjuvant chemotherapy (NAC). The identification of biomarkers to predict NAC response and inform personalized treatment strategies is essential. In this study, we conducted large-scale gene expression meta-analyses to identify genes associated with NAC response and survival outcomes. The results showed that immune, cell cycle/mitotic, and RNA splicing-related pathways were significantly associated with favorable clinical outcomes. Furthermore, we integrated and divided the gene association results from NAC response and survival outcomes into four quadrants, which provided more insights into potential NAC response mechanisms and biomarker discovery.
Language	English
Publishing date	2023-04-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15082194
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Article ; Online: Site of Cholesterol Oxidation Impacts Its Localization and Domain Formation in the Neuronal Plasma Membrane.

Wilson, Katie A / Wang, Lily / O'Mara, Megan L

ACS chemical neuroscience

2021 Volume 12, Issue 20, Page(s) 3873–3884

Abstract: Cholesterol is integral to the structure of mammalian cell membranes. Oxidation of cholesterol alters how it behaves in the membrane and influences the membrane biophysical properties. Elevated levels of oxidized cholesterol are associated with ... ...

Abstract	Cholesterol is integral to the structure of mammalian cell membranes. Oxidation of cholesterol alters how it behaves in the membrane and influences the membrane biophysical properties. Elevated levels of oxidized cholesterol are associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, and Huntington's disease. Previous work has investigated the impact of oxidized cholesterol in the context of simple model membrane systems. However, there is a growing body of literature that shows that complex membranes possessing physiological phospholipid distributions have different properties from those of binary or trinary model membranes. In the current work, the impact of oxidized cholesterol on the biophysical properties of a complex neuronal plasma membrane is investigated using coarse-grained Martini molecular dynamics simulations. Comparison of the native neuronal membrane to neuronal membranes containing 10% tail-oxidized or 10% head-oxidized cholesterol shows that the site of oxidization changes the behavior of the oxidized cholesterol in the membrane. Furthermore, species-specific domain formation is observed between each oxidized cholesterol and minor lipid classes. Although both tail-oxidized and head-oxidized cholesterols modulate the biophysical properties of the membrane, smaller changes are observed in the complex neuronal membrane than seen in the previous work on simple binary or trinary model membranes. This work highlights the presence of compensatory effects of lipid diversity in the complex neuronal membrane. Overall, this study improves our molecular-level understanding of the effects of oxidized cholesterol on the properties of neuronal tissue and emphasizes the importance of studying membranes with realistic lipid compositions.
MeSH term(s)	Animals ; Cell Membrane ; Cholesterol ; Lipid Bilayers ; Molecular Dynamics Simulation ; Oxidation-Reduction
Chemical Substances	Lipid Bilayers ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2021-10-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1948-7193
ISSN (online)	1948-7193
DOI	10.1021/acschemneuro.1c00395
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Article ; Online: Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein.

Wang, Lily / O'Mara, Megan L

Journal of chemical theory and computation

2021 Volume 17, Issue 10, Page(s) 6491–6508

Abstract: Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has ... ...

Abstract	Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarse-grained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein-membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and cross-linking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.
MeSH term(s)	ATP Binding Cassette Transporter, Subfamily B/chemistry ; Humans ; Molecular Dynamics Simulation ; Peptides/chemistry ; Protein Structure, Secondary ; Proteins
Chemical Substances	ATP Binding Cassette Transporter, Subfamily B ; Peptides ; Proteins
Language	English
Publishing date	2021-09-10
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.1c00414
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