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Article ; Online: ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses.

Watford, Sean / Ly Pham, Ly / Wignall, Jessica / Shin, Robert / Martin, Matthew T / Friedman, Katie Paul

Reproductive toxicology (Elmsford, N.Y.)

2019 Volume 89, Page(s) 145–158

Abstract: The Toxicity Reference Database (ToxRefDB) structures information from over 5000 in vivo toxicity studies, conducted largely to guidelines or specifications from the US Environmental Protection Agency and the National Toxicology Program, into a public ... ...

Abstract	The Toxicity Reference Database (ToxRefDB) structures information from over 5000 in vivo toxicity studies, conducted largely to guidelines or specifications from the US Environmental Protection Agency and the National Toxicology Program, into a public resource for training and validation of predictive models. Herein, ToxRefDB version 2.0 (ToxRefDBv2) development is described. Endpoints were annotated (e.g. required, not required) according to guidelines for subacute, subchronic, chronic, developmental, and multigenerational reproductive designs, distinguishing negative responses from untested. Quantitative data were extracted, and dose-response modeling for nearly 28,000 datasets from nearly 400 endpoints using Benchmark Dose (BMD) Modeling Software were generated and stored. Implementation of controlled vocabulary improved data quality; standardization to guideline requirements and cross-referencing with United Medical Language System (UMLS) connects ToxRefDBv2 observations to vocabularies linked to UMLS, including PubMed medical subject headings. ToxRefDBv2 allows for increased connections to other resources and has greatly enhanced quantitative and qualitative utility for predictive toxicology.
MeSH term(s)	Animals ; Computational Biology/methods ; Computational Biology/trends ; Databases, Factual/trends ; Dose-Response Relationship, Drug ; Hazardous Substances/chemistry ; Hazardous Substances/classification ; Hazardous Substances/toxicity ; Models, Biological ; Software ; Toxicology/methods ; Toxicology/trends ; United States ; United States Environmental Protection Agency
Chemical Substances	Hazardous Substances
Language	English
Publishing date	2019-07-21
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	639342-1
ISSN	1873-1708 ; 0890-6238
ISSN (online)	1873-1708
ISSN	0890-6238
DOI	10.1016/j.reprotox.2019.07.012
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pseudo-Hydrodynamic Flow of Quasiparticles in Semimetal WTe

Choi, Young-Gwan / Doan, Manh-Ha / Ngoc, Luu Ly Pham / Lee, Junsu / Choi, Gyung-Min / Chernodub, Maxim Nikolaevich

Small (Weinheim an der Bergstrasse, Germany)

2023 Volume 19, Issue 27, Page(s) e2206604

Abstract: Recently, much interest has emerged in fluid-like electric charge transport in various solid-state systems. The hydrodynamic behavior of the electronic fluid reveals itself as a decrease of the electrical resistance with increasing temperature (the ... ...

Abstract	Recently, much interest has emerged in fluid-like electric charge transport in various solid-state systems. The hydrodynamic behavior of the electronic fluid reveals itself as a decrease of the electrical resistance with increasing temperature (the Gurzhi effect) in narrow channels, polynomial scaling of the resistance as a function of the channel width, violation of the Wiedemann-Franz law supported by the emergence of the Poiseuille flow. Similar to whirlpools in flowing water, the viscous electronic flow generates vortices, resulting in abnormal sign-changing electrical response driven by backflow. However, the question of whether the long-ranged sign-changing electrical response can be produced by a mechanism other than hydrodynamics has not been addressed so far. Here polarization-sensitive laser microscopy is used to demonstrate the emergence of visually similar abnormal sign-alternating patterns in semi-metallic tungsten ditelluride at room temperature where this material does not exhibit true hydrodynamics. It is found that the neutral quasiparticle current consisting of electrons and holes obeys an equation remarkably similar to the Navier-Stokes equation. In particular, the momentum relaxation is replaced by the much slower process of quasiparticle recombination. This pseudo-hydrodynamic flow of quasiparticles leads to a sign-changing charge accumulation pattern via different diffusivities of electrons and holes.
Language	English
Publishing date	2023-03-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202206604
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Variability in

Ly Pham, Ly / Watford, Sean / Pradeep, Prachi / Martin, Matthew T / Thomas, Russell / Judson, Richard / Setzer, R Woodrow / Paul Friedman, Katie

Computational toxicology (Amsterdam, Netherlands)

2020 Volume 15, Issue August 2020, Page(s) 1–100126

Abstract: New approach methodologies (NAMs) for chemical hazard assessment are often evaluated via comparison to animal studies; however, variability in animal study data limits NAM accuracy. The US EPA Toxicity Reference Database (ToxRefDB) enables consideration ... ...

Abstract	New approach methodologies (NAMs) for chemical hazard assessment are often evaluated via comparison to animal studies; however, variability in animal study data limits NAM accuracy. The US EPA Toxicity Reference Database (ToxRefDB) enables consideration of variability in effect levels, including the lowest effect level (LEL) for a treatment-related effect and the lowest observable adverse effect level (LOAEL) defined by expert review, from subacute, subchronic, chronic, multi-generation reproductive, and developmental toxicity studies. The objectives of this work were to quantify the variance within systemic LEL and LOAEL values, defined as potency values for effects in adult or parental animals only, and to estimate the upper limit of NAM prediction accuracy. Multiple linear regression (MLR) and augmented cell means (ACM) models were used to quantify the total variance, and the fraction of variance in systemic LEL and LOAEL values explained by available study descriptors (e.g., administration route, study type). The MLR approach considered each study descriptor as an independent contributor to variance, whereas the ACM approach combined categorical descriptors into cells to define replicates. Using these approaches, total variance in systemic LEL and LOAEL values (in log
Language	English
Publishing date	2020-05-28
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-1113
ISSN	2468-1113
DOI	10.1016/j.comtox.2020.100126
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The relationship between international tourist arrivals and foreign direct investment

Ly-Pham ThiMinh / Hieu-LeMinh / Phung-Tran ThiPhi

Acta oeconomica Pragensia : vědecký časopis Vysoke Školy Ekonomické v Praze Vol. 25, No. 4 , p. 3-12

a granger causality analysis

2017 Volume 25, Issue 4, Page(s) 3–12

Author's details	Ly-Pham ThiMinh, Hieu-LeMinh, Phung-Tran ThiPhi
Keywords	foreign direct investment ; granger causality ; international tourist arrivals
Language	English
Publishing place	Praha
Document type	Article
ZDB-ID	959721-9 ; 2559686-X
ISSN	1804-2112 ; 0572-3043
ISSN (online)	1804-2112
ISSN	0572-3043
Database	ECONomics Information System

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Article ; Online: High-Throughput Screening Assay for Detecting Drug-Induced Changes in Synchronized Neuronal Oscillations and Potential Seizure Risk Based on Ca 2+ Fluorescence Measurements in Human Induced Pluripotent Stem Cell (hiPSC)-Derived Neuronal 2D and 3D Cultures

Hua-Rong Lu / Manabu Seo / Mohamed Kreir / Tetsuya Tanaka / Rie Yamoto / Cristina Altrocchi / Karel van Ammel / Fetene Tekle / Ly Pham / Xiang Yao / Ard Teisman / David J. Gallacher

Cells, Vol 12, Iss 958, p

2023 Volume 958

Abstract: Drug-induced seizure liability is a significant safety issue and the basis for attrition in drug development. Occurrence in late development results in increased costs, human risk, and delayed market availability of novel therapeutics. Therefore, there ... ...

Abstract	Drug-induced seizure liability is a significant safety issue and the basis for attrition in drug development. Occurrence in late development results in increased costs, human risk, and delayed market availability of novel therapeutics. Therefore, there is an urgent need for biologically relevant, in vitro high-throughput screening assays (HTS) to predict potential risks for drug-induced seizure early in drug discovery. We investigated drug-induced changes in neural Ca 2+ oscillations, using fluorescent dyes as a potential indicator of seizure risk, in hiPSC-derived neurons co-cultured with human primary astrocytes in both 2D and 3D forms. The dynamics of synchronized neuronal calcium oscillations were measured with an FDSS kinetics reader. Drug responses in synchronized Ca 2+ oscillations were recorded in both 2D and 3D hiPSC-derived neuron/primary astrocyte co-cultures using positive controls (4-aminopyridine and kainic acid) and negative control (acetaminophen). Subsequently, blinded tests were carried out for 25 drugs with known clinical seizure incidence. Positive predictive value (accuracy) based on significant changes in the peak number of Ca 2+ oscillations among 25 reference drugs was 91% in 2D vs. 45% in 3D hiPSC-neuron/primary astrocyte co-cultures. These data suggest that drugs that alter neuronal activity and may have potential risk for seizures can be identified with high accuracy using an HTS approach using the measurements of Ca 2+ oscillations in hiPSC-derived neurons co-cultured with primary astrocytes in 2D.
Keywords	hiPSC neurons ; 2D ; 3D ; high throughput screening HTS ; Ca 2+ neuronal oscillations ; neuronal active drugs ; Biology (General) ; QH301-705.5
Subject code	333
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Improving Efficiency Assessment of Psychiatric Halfway Houses: A Context-Dependent Data Envelopment Analysis Approach.

Shen, Chien-Wen / Hsu, Chin-Hsing / Lung, For-Wey / Ly, Pham Thi Minh

Healthcare (Basel, Switzerland)

2020 Volume 8, Issue 3

Abstract: This study proposes the approach of context-dependent data envelopment analysis (DEA) to measure operating performance in halfway houses to enable suitable adjustments at the current economic scale. The proposed approach can be used to discriminate the ... ...

Abstract	This study proposes the approach of context-dependent data envelopment analysis (DEA) to measure operating performance in halfway houses to enable suitable adjustments at the current economic scale. The proposed approach can be used to discriminate the performance of efficient halfway houses and provide more accurate DEA results related to the performance of all halfway houses in a region or a country. The relative attractiveness and progress were also evaluated, and individual halfway houses' competitive advantage and potential competitors could be determined. A case study of 38 halfway houses in Taiwan was investigated by our proposed approach. Findings suggest that fifteen halfway houses belong to the medium level, which can be classified into a quadrant by examining both their attractiveness score and progress score. The results can be used to allocate community resources to improve the operational directions and develop incentives for halfway houses with attractive and progressive values, which can reduce the institutionalization and waste of medical resources caused by the long-term hospitalization of patients with mental illnesses. Our proposed approach can also provide references for operators and policy makers to improve the management, accreditation, and resource allocation of institutions.
Language	English
Publishing date	2020-06-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2721009-1
ISSN	2227-9032
ISSN	2227-9032
DOI	10.3390/healthcare8030189
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Chemical Waste Management in the U.S. Semiconductor Industry

Shen, Chien-wen / Minh Ly, Pham Thi / Tran, Phung Phi

Sustainability. 2018 May 13, v. 10, no. 5

2018

Abstract: Sustainability has become the biggest concern of the semiconductor industry because of hundreds of high-purity organic and inorganic compounds involved in manufacturing semiconductors not being treated economically. The aim of this study was to ... ...

Abstract	Sustainability has become the biggest concern of the semiconductor industry because of hundreds of high-purity organic and inorganic compounds involved in manufacturing semiconductors not being treated economically. The aim of this study was to understand how semiconductor companies manage their chemical wastes, by analyzing the U.S. Environmental Protection Agency’s Toxics Release Inventory data for hydrogen fluoride, nitric acid, ammonia, N-methyl-2-pyrrolidone, hydrochloric acid, nitrate compounds, and sulfuric acid. Cluster analysis was adopted to classify the U.S. semiconductor companies into different performance groups according to their waste management approaches. On the basis of the results, twenty-seven companies were classified in the “best performance” category for the waste management of two or more chemicals. However, 15 companies were classified in the worst performance categories. The semiconductor companies can refer to our results to understand their performance and which companies they should benchmark regarding chemical waste management. City governments can also refer to our results to employ suitable policies to reduce the negative impacts of the chemical waste from regional semiconductor companies.
Keywords	ammonia ; business enterprises ; cluster analysis ; environmental protection ; hydrochloric acid ; hydrofluoric acid ; inventories ; issues and policy ; manufacturing ; nitrates ; nitric acid ; semiconductors ; sulfuric acid ; waste management ; wastes ; United States
Language	English
Dates of publication	2018-0513
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518383-7
ISSN	2071-1050
ISSN	2071-1050
DOI	10.3390/su10051545
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii.

M Indriati Hood-Pishchany / Ly Pham / Christiaan D Wijers / William J Burns / Kelli L Boyd / Lauren D Palmer / Eric P Skaar / Michael J Noto

PLoS Pathogens, Vol 16, Iss 3, p e

2020 Volume 1008374

Abstract: Antimicrobial resistance is increasing in pathogenic bacteria. Yet, the effect of antibiotic exposure on resistant bacteria has been underexplored and may affect pathogenesis. Here we describe the discovery that propagation of the human pathogen ... ...

Abstract	Antimicrobial resistance is increasing in pathogenic bacteria. Yet, the effect of antibiotic exposure on resistant bacteria has been underexplored and may affect pathogenesis. Here we describe the discovery that propagation of the human pathogen Acinetobacter baumannii in an aminoglycoside antibiotic results in alterations to the bacterium that interact with lung innate immunity resulting in enhanced bacterial clearance. Co-inoculation of mice with A. baumannii grown in the presence and absence of the aminoglycoside, kanamycin, induces enhanced clearance of a non-kanamycin-propagated strain. This finding can be replicated when kanamycin-propagated A. baumannii is killed prior to co-inoculation of mice, indicating the enhanced bacterial clearance results from interactions with innate host defenses in the lung. Infection with kanamycin-propagated A. baumannii alters the kinetics of phagocyte recruitment to the lung and reduces pro- and anti-inflammatory cytokine and chemokine production in the lung and blood. This culminates in reduced histopathologic evidence of lung injury during infection despite enhanced bacterial clearance. Further, the antibacterial response induced by killed aminoglycoside-propagated A. baumannii enhances the clearance of multiple clinically relevant Gram-negative pathogens from the lungs of infected mice. Together, these findings exemplify cooperation between antibiotics and the host immune system that affords protection against multiple antibiotic-resistant bacterial pathogens. Further, these findings highlight the potential for the development of a broad-spectrum therapeutic that exploits a similar mechanism to that described here and acts as an innate immunity modulator.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Subject code	630
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Interleukin-23 receptor signaling impairs the stability and function of colonic regulatory T cells

Justin Jacobse / Rachel E. Brown / Jing Li / Jennifer M. Pilat / Ly Pham / Sarah P. Short / Christopher T. Peek / Andrea Rolong / M. Kay Washington / Ruben Martinez-Barricarte / Mariana X. Byndloss / Catherine Shelton / Janet G. Markle / Yvonne L. Latour / Margaret M. Allaman / James E. Cassat / Keith T. Wilson / Yash A. Choksi / Christopher S. Williams /

Ken S. Lau / Charles R. Flynn / Jean-Laurent Casanova / Edmond H.H.M. Rings / Janneke N. Samsom / Jeremy A. Goettel

Cell Reports, Vol 42, Iss 2, Pp 112128- (2023)

2023

Abstract: Summary: The cytokine interleukin-23 (IL-23) is involved in the pathogenesis of inflammatory and autoimmune conditions including inflammatory bowel disease (IBD). IL23R is enriched in intestinal Tregs, yet whether IL-23 modulates intestinal Tregs remains ...

Abstract	Summary: The cytokine interleukin-23 (IL-23) is involved in the pathogenesis of inflammatory and autoimmune conditions including inflammatory bowel disease (IBD). IL23R is enriched in intestinal Tregs, yet whether IL-23 modulates intestinal Tregs remains unknown. Here, investigating IL-23R signaling in Tregs specifically, we show that colonic Tregs highly express Il23r compared with Tregs from other compartments and their frequency is reduced upon IL-23 administration and impairs Treg suppressive function. Similarly, colonic Treg frequency is increased in mice lacking Il23r specifically in Tregs and exhibits a competitive advantage over IL-23R-sufficient Tregs during inflammation. Finally, IL-23 antagonizes liver X receptor pathway, cellular cholesterol transporter Abca1, and increases Treg apoptosis. Our results show that IL-23R signaling regulates intestinal Tregs by increasing cell turnover, antagonizing suppression, and decreasing cholesterol efflux. These results suggest that IL-23 negatively regulates Tregs in the intestine with potential implications for promoting chronic inflammation in patients with IBD.
Keywords	CP: Immunology ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Arc Thermal Spray NiCr20 Alloy Coating

Van Tuan Nguyen / Quy Le Thu / Tuan Anh Nguyen / Quoc Cuong Ly / Ly Pham Thi / Ha Pham Thi / Thanh Dinh Thi Mai

International Journal of Electrochemistry, Vol

Fabrication, Sealant, Heat Treatment, Wear, and Corrosion Resistances

2019 Volume 2019

Abstract: This study presents the effect of heat treatment on porosity, phase composition, microhardness, and wear and corrosion resistances of the thermal sprayed NiCr20 coating after sealing with aluminum phosphate. The annealing temperatures were varied in a ... ...

Abstract	This study presents the effect of heat treatment on porosity, phase composition, microhardness, and wear and corrosion resistances of the thermal sprayed NiCr20 coating after sealing with aluminum phosphate. The annealing temperatures were varied in a range of 400 to 1000°C. The obtained results indicated the porosity of coating decreased with increasing the annealing temperature. After treatment at temperatures in range of 800-1000°C, more than 90% of initial pores in the coating were successfully filled with the sealants. The XRD data revealed not only the formation of new phases of other compounds, but also the interaction between coating and sealant. After heat treatment, wear resistance of coating was 12 times higher than that without heat treatment. The corrosion test in H2SO4 solution indicated that the presence of sealant in coatings increased their corrosion resistance. From these findings, application of these NiCr20 coatings to protect steel against wear and corrosion appears very promising.
Keywords	Chemistry ; QD1-999
Subject code	669 ; 620
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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