Publications by authors named "Jagat Rathod"

13 Publications

  • Page 1 of 1

YPIBP: A repository for phosphoinositide-binding proteins in yeast.

Comput Struct Biotechnol J 2021 24;19:3692-3707. Epub 2021 Jun 24.

Department of Electrical Engineering, College of Electrical Engineering and Computer Science, National Cheng Kung University, Tainan 701, Taiwan.

Phosphoinositides (PIs) are a family of eight lipids consisting of phosphatidylinositol (PtdIns) and its seven phosphorylated forms. PIs have important regulatory functions in the cell including lipid signaling, protein transport, and membrane trafficking. Yeast has been recognized as a eukaryotic model system to study lipid-protein interactions. Hundreds of yeast PI-binding proteins have been identified, but this research knowledge remains scattered. Besides, the complete PI-binding spectrum and potential PI-binding domains have not been interlinked. No comprehensive databases are available to support the lipid-protein interaction research on phosphoinositides. Here we constructed the first knowledgebase of Yeast Phosphoinositide-Binding Proteins (YPIBP), a repository consisting of 679 PI-binding proteins collected from high-throughput proteome-array and lipid-array studies, QuickGO, and a rigorous literature mining. The YPIBP also contains protein domain information in categories of lipid-binding domains, lipid-related domains and other domains. The YPIBP provides search and browse modes along with two enrichment analyses (PI-binding enrichment analysis and domain enrichment analysis). An interactive visualization is given to summarize the PI-domain-protein interactome. Finally, three case studies were given to demonstrate the utility of YPIBP. The YPIBP knowledgebase consolidates the present knowledge and provides new insights of the PI-binding proteins by bringing comprehensive and in-depth interaction network of the PI-binding proteins. YPIBP is available at http://cosbi7.ee.ncku.edu.tw/YPIBP/.
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http://dx.doi.org/10.1016/j.csbj.2021.06.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8261538PMC
June 2021

Clostridioides difficile spores stimulate inflammatory cytokine responses and induce cytotoxicity in macrophages.

Anaerobe 2021 May 31;70:102381. Epub 2021 May 31.

Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA; Oklahoma State University College of Osteopathic Medicine at Cherokee Nation, Tahlequah, OK, USA. Electronic address:

Clostridioides difficile is a gram-positive, spore-forming anaerobic bacterium, and the leading cause of antibiotic-associated diarrhea worldwide. During C. difficile infection, spores germinate in the presence of bile acids into vegetative cells that subsequently colonize the large intestine and produce toxins. In this study, we demonstrated that C. difficile spores can universally adhere to, and be phagocytosed by, murine macrophages. Only spores from toxigenic strains were able to significantly stimulate the production of inflammatory cytokines by macrophages and subsequently induce significant cytotoxicity. Spores from the isogenic TcdA and TcdB double mutant induced significantly lower inflammatory cytokines and cytotoxicity in macrophages, and these activities were restored by pre-exposure of the spores to either toxins. These findings suggest that during sporulation, spores might be coated with C. difficile toxins from the environment, which could affect C. difficile pathogenesis in vivo.
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http://dx.doi.org/10.1016/j.anaerobe.2021.102381DOI Listing
May 2021

Systematic Analysis of Phosphatidylinositol-5-phosphate-Interacting Proteins Using Yeast Proteome Microarrays.

Anal Chem 2021 01 11;93(2):868-877. Epub 2020 Dec 11.

Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan.

We used yeast proteome microarrays (∼5800 purified proteins) to conduct a high-throughput and systematic screening of PI5P-interacting proteins with PI5P-tagged fluorescent liposomal nanovesicles. Lissamine rhodamine B-dipalmitoyl phosphatidylethanol was incorporated into the liposome bilayer to provide the nanovesicles with fluorescence without any encapsulants, which not only made the liposome fabrication much easier without the need for purification but also improved the chip-probing quality. A special chip assay was washed very gently without the traditional spin-dry step. Forty-five PI5P-interacting proteins were identified in triplicate with this special chip assay. Subsequently, we used flow cytometry to validate these interactions, and a total of 41 PI5P-interacting proteins were confirmed. Enrichment analysis revealed that these proteins have significant functions associated with ribosome biogenesis, rRNA processing, ribosome binding, GTP binding, and hydrolase activity. Their component enrichment is located in the nucleolus. The InterPro domain analysis indicated that PI5P-interacting proteins are enriched in the P-loop containing nucleoside triphosphate hydrolases domain (P-loop). Additionally, using the MEME program, we identified a consensus motif (IVGPAGTGKSTLF) that contains the Walker A sequence, a well-known nucleotide-binding motif. Furthermore, using a quartz crystal microbalance, both the consensus motif and Walker A motif showed strong affinities to PI5P-containing liposomes but not to PI5P-deprived liposomes or PI-containing liposomes. Additionally, the glycine (G6) and lysine (K7) residues of the Walker A motif (-GPAGTGKS-) were found to be critical to the PI5P-binding ability. This study not only identified an additional set of PI5P-interacting proteins but also revealed the strong PI5P-binding affinity ( = 1.81 × 10 M) of the Walker A motif beyond the motif's nucleotide-binding characteristic.
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http://dx.doi.org/10.1021/acs.analchem.0c03463DOI Listing
January 2021

Systematic changes of bone hydroxyapatite along a charring temperature gradient: An integrative study with dissolution behavior.

Sci Total Environ 2021 Apr 3;766:142601. Epub 2020 Oct 3.

Material Science Group, National Synchrotron Radiation Research Center, Hsinchu, Taiwan.

The applicability of bone char as a long-term phosphorus nutrient source was assessed by integrating their mineral transformation and physicochemical properties with their dissolution behavior. We have explored synchrotron-based spectroscopic and imaging techniques (FTIR, XRD, and TXM) to investigate the physicochemical changes of bone and bone char along a charring temperature gradient (300-1200 °C) and used a lab incubation experiment to study their dissolution behaviors in solutions of different pH (4, 6, and 6.9). The thermal decomposition of inorganic carbonate (CO) and the loss of organic components rendered a crystallographic rearrangement (blueshift of the PO peak) and mineral transformation with increasing temperatures. The mineral transformation from B-type to AB- and A-type carbonate substitution occurred mainly at <700 °C, while the transformation from carbonated hydroxyapatite (CHAp) to more mineralogically and chemically stable HAp occurred at >800 °C. The loss of inorganic carbonate and the increase of structural OH with increasing temperatures explained the change of pH buffering capacity and increase of pH and their dissolution behaviors. The higher peak area ratios of phosphate to carbonate and phosphate to amide I band with increasing temperatures corroborated the higher stability and resistivity to acidic dissolution by bone chars made at higher temperatures. Our findings suggest that bone char made at low to intermediate temperatures can be a substantial source of phosphorus for soil fertility via waste management and recycling. The bone char made at 500 °C exhibited a high pH buffering capacity in acidic and near-neutral solutions. The 700 °C bone char was proposed as a suitable liming agent for raising the soil pH and abating soil acidity. Our study has underpinned the systematic changes of bone char and interlinked the charring effect with their dissolution behavior, providing a scientific base for understanding the applicability of different bone chars as suitable P-fertilizers.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142601DOI Listing
April 2021

Black carbon enriches short-range-order ferrihydrite in Amazonian Dark Earth: Interplay mechanism and environmental implications.

Sci Total Environ 2020 Jul 24;725:138195. Epub 2020 Mar 24.

Life Science Group, National Synchrotron Radiation Center, Hsinchu, Taiwan; Department of Optics and Photonics, National Central University, Chung-Li, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan. Electronic address:

Our study underpins the mechanism of organo-mineral interaction between black carbon (BC, biochar) and associated minerals in the historical BC-rich Amazonian Dark Earth (ADE) by using synchrotron-based microscopic (TXM), microspectroscopic (μFTIR) and spectroscopic (XAS and μ-diffraction) approaches. The BC-rich ADE contained over 100% more poorly crystalline minerals than the adjacent tropical soil. Linear combination fitting of k-spacing in the X-ray Absorption Spectra (XAS) revealed that ferrihydrite contributed to 81.1% of the Fe-minerals in BC. A small but distinct peak was observed at 5.7 Å in the extended X-ray absorption fine structure k oscillation of BC, revealing the presence of FeC (including Fe-O-C) covalent bonds. No FeC path was yielded by the XAS fitting when an obvious peak downshift of the first (FeFe) shell was observed, suggesting that the availability of inner-sphere FeC complexation was limited to the BC surface and interphase region. The main minerals for organo-mineral complexation were short-range-order (SRO) ferrihydrite on BC instead of corner-sharing FeO octahedra. Compared to ADE, the coordination number of the first (FeFe) and second (FeFe) shell was higher in BC, revealing a higher degree of order in coordination between the neighboring Fe mineral crystals. Black C limited the progressive aging of amorphous Fe phases and greatly enriched SRO ferrihydrite in the redox-fluctuating and high-leaching environment. The transformation of SRO ferrihydrite into the more crystalline Fe oxides was controlled by the local pH environment. A strong signal from the complexed phenolic group (aryl-OH, 1241 cm) and a distinct band of inner-sphere complexation (Fe-aryl C, 1380-1384 cm) were identified in the FTIR spectra. The enrichment of poorly crystalline minerals can have positive feedback on the long-term stabilization of BC. The scale-up application of biochar to agricultural and ecological systems may have a long-lasting impact on the enrichment and transformation of the SRO minerals in the soil.
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http://dx.doi.org/10.1016/j.scitotenv.2020.138195DOI Listing
July 2020

The Transcriptional Regulator Lrp Contributes to Toxin Expression, Sporulation, and Swimming Motility in .

Front Cell Infect Microbiol 2019 17;9:356. Epub 2019 Oct 17.

Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.

is a Gram-positive, spore-forming bacterium, and major cause of nosocomial diarrhea. Related studies have identified numerous factors that influence virulence traits such as the production of the two primary toxins, toxin A (TcdA) and toxin B (TcdB), as well as sporulation, motility, and biofilm formation. However, multiple putative transcriptional regulators are reportedly encoded in the genome, and additional factors are likely involved in virulence regulation. Although the leucine-responsive regulatory protein (Lrp) has been studied extensively in Gram-negative bacteria, little is known about its function in Gram-positive bacteria, although homologs have been identified in the genome. This study revealed that disruption of the lone homolog in decelerated growth under nutrient-limiting conditions, increased TcdA and TcdB production. Lrp was also found to negatively regulate sporulation while positively regulate swimming motility in strain R20291, but not in strain 630. The Lrp appeared to function through transcriptional repression or activation. In addition, the mutant was relatively virulent in a mouse model of infection. The results of this study collectively demonstrated that Lrp has broad regulatory function in toxin expression, sporulation, motility, and pathogenesis.
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http://dx.doi.org/10.3389/fcimb.2019.00356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811523PMC
June 2020

Micro-colonization of arsenic-resistant Staphylococcus sp. As-3 on arsenopyrite (FeAsS) drives arsenic mobilization under anoxic sub-surface mimicking conditions.

Sci Total Environ 2019 Jun 8;669:527-539. Epub 2019 Mar 8.

National Synchrotron Radiation Research Center, Life Science Group, Hsinchu 30076, Taiwan; Department of Optics and Photonics, National Central University, Chung-Li District, Taoyuan City 32001, Taiwan.

We investigated the subsurface biomatrix of the most abundant As-mineral, arsenopyrite (FeAsS), and meticulously studied a potential biogenic arsenic mobilization phenomenon. An arsenic-resistant [up to 7.5 mM As(III) and 200 mM As(V)] and arsenate-reducing bacterial strain (Staphylococcus sp. As-3) was isolated from a sediment core sample taken from the Budai borehole, on the southwestern coast of Taiwan. Isolate As-3 could reduce 5 mM As(V) to 3.04 mM in 96 h, generating 1.6 mM As(III) under anoxic conditions. Isolate As-3, which adsorbed As(V) up to 19.02 mg g (cdw) and As(III) up to 0.46 mg g (cdw), demonstrated effective As-bioaccumulating ability, as corroborated by a TEM-EDS analysis. Under anaerobic batch conditions, isolate As-3 micro-colonies could grow on as well as interact with arsenopyrite (FeAsS), mobilizing arsenic into soluble phase as As(III) and As(V). Using synchrotron radiation-based FTIR micro-spectroscopy, various functional group signatures and critical chemical bonds enabling a direct interaction with arsenopyrite were underpinned, such as a potential P-OFe bond involved in facilitating bacteria-mineral interaction. Using atomic force microscopy, we analyzed the scattered bacterial cell arrangement and structure and measured various biomechanical properties of micro-colonized Staphylococcus sp. As-3 cells on arsenopyrite. We suggest that the release of organic acids from As-3 drives soluble arsenic release in the aqueous phase under anoxic conditions through oxidative dissolution. Furthermore, arsC-encoding putative cytoplasmic arsenic reductase sequencing and transcript characterization indicated that arsC plays a possible role in the reduction of moderately soluble As(V) to highly soluble toxic As(III) under anoxic conditions. Thus, we suggest that firmicutes such as Staphylococcus sp. As-3 may play an important role in microbially-mediated arsenic mobilization, leading to arsenic release in the sub-surface niche.
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http://dx.doi.org/10.1016/j.scitotenv.2019.03.084DOI Listing
June 2019

The whole genome insight on condition-specific redox activity and arsenopyrite interaction promoting As-mobilization by strain Lysinibacillus sp. B2A1.

J Hazard Mater 2019 02 23;364:671-681. Epub 2018 Oct 23.

Department of Earth Sciences, National Cheng Kung University, 1st University Road, Tainan, 70101, Taiwan.

A gram-positive spore former, Lysinibacillus sp. B2A1 was isolated from a high arsenic containing groundwater of Beimen2A well, Chianan Plain area, Southwestern Taiwan. Noteworthy, in the subsurface-mimicking anoxic incubation with a Na-lactate amendment system, this isolate could interact with arsenic-source mineral arsenopyrite and enhance arsenic mobilization. Further, the isolate showed elevated levels of arsenic resistance, 200 mM and 7.5 mM for arsenate and arsenite, respectively. Lysinibacillus sp. B2A1 demonstrated condition-specific redox activities including salient oxic oxidation of arsenite and anoxic reduction of arsenate. The elevated rate of As(III) oxidation (V = 0.13 μM min per 10 cells, K = 15.3 μM) under oxic conditions was potent. Correlating with stout persistence in an arsenic-rich niche, remarkably, the lesser toxic effects of arsenic ions on bacterial sporulation frequency and germination highlight this strain's ability to thrive under catastrophic conditions. Moreover, the whole genome analysis elucidated diverse metal redox/resistance genes that included a potential arsenite S-adenosylmethyltransferase capable of mitigating arsenite toxicity. Owing to its arsenic resistance, conditional redox activities and ability to interact with arsenic minerals leading to arsenic mobilization, the presence of such spore-forming strains could be a decisive indication towards arsenic mobilization in subsurface aquifers having a high concentration of soluble arsenic or its source minerals.
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http://dx.doi.org/10.1016/j.jhazmat.2018.10.042DOI Listing
February 2019

YARG: A repository for arsenic-related genes in yeast.

PLoS One 2018 26;13(7):e0201204. Epub 2018 Jul 26.

Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan.

Arsenic is a toxic metalloid. Moderate levels of arsenic exposure from drinking water can cause various human health problems such as skin lesions, circulatory disorders and cancers. Thus, arsenic toxicity is a key focus area for environmental and toxicological investigations. Many arsenic-related genes in yeast have been identified by experimental strategies such as phenotypic screening and transcriptional profiling. These identified arsenic-related genes are valuable information for studying arsenic toxicity. However, the literature about these identified arsenic-related genes is widely dispersed and cannot be easily acquired by researchers. This prompts us to develop YARG (Yeast Arsenic-Related Genes) database, which comprehensively collects 3396 arsenic-related genes in the literature. For each arsenic-related gene, the number and types of experimental evidence (phenotypic screening and/or transcriptional profiling) are provided. Users can use both search and browse modes to query arsenic-related genes in YARG. We used two case studies to show that YARG can return biologically meaningful arsenic-related information for the query gene(s). We believe that YARG is a useful resource for arsenic toxicity research. YARG is available at http://cosbi4.ee.ncku.edu.tw/YARG/.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201204PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062094PMC
January 2019

Lauric Acid Is an Inhibitor of Growth and Reduces Inflammation in a Mouse Infection Model.

Front Microbiol 2017 17;8:2635. Epub 2018 Jan 17.

Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.

is a Gram-positive, spore-forming anaerobic human gastrointestinal pathogen. infection (CDI) is a major health concern worldwide, with symptoms ranging from diarrhea to pseudomembranous colitis, toxic megacolon, sepsis, and death. CDI onset and progression are mostly caused by intestinal dysbiosis and exposure to spores. Current treatment strategies include antibiotics; however, antibiotic use is often associated with high recurrence rates and an increased risk of antibiotic resistance. Medium-chain fatty acids (MCFAs) have been revealed to inhibit the growth of multiple human bacterial pathogens. Components of coconut oil, which include lauric acid, have been revealed to inhibit growth . In this study, we demonstrated that lauric acid exhibits potent antimicrobial activities against multiple toxigenic isolates . The inhibitory effect of lauric acid is partly due to reactive oxygen species (ROS) generation and cell membrane damage. The administration of lauric acid considerably reduced biofilm formation and preformed biofilms in a dose-dependent manner. Importantly, in a mouse infection model, lauric acid pretreatment reduced CDI symptoms and proinflammatory cytokine production. Our combined results suggest that the naturally occurring MCFA lauric acid is a novel inhibitor and is useful in the development of an alternative or adjunctive treatment for CDI.
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http://dx.doi.org/10.3389/fmicb.2017.02635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776096PMC
January 2018

Arsenite-oxidizing bacteria exhibiting plant growth promoting traits isolated from the rhizosphere of Oryza sativa L.: Implications for mitigation of arsenic contamination in paddies.

J Hazard Mater 2016 Jan 25;302:10-18. Epub 2015 Sep 25.

Department of Earth Sciences, National Cheng Kung University, Tainan, Taiwan.

Arsenite-oxidizing bacteria exhibiting plant growth promoting (PGP) traits can have the advantages of reducing As-uptake by rice and promoting plant growth in As-stressed soil. A gram-positive bacterium Bacillus flexus ASO-6 resistant to high levels of As (32 and 280 mM for arsenite and arsenate, respectively) and exhibiting elevated rates of As(III) oxidation (Vmax=1.34 μM min(-1) 10(-7) cell) was isolated from rhizosphere of rice. The presence of aoxB gene and exhibition of As(III)-oxidase enzyme activity of this strain was observed. The ability of the strain to produce siderophore, IAA, ACC-deaminase and to solubilize phosphate was verified. The rice seed treated with the strain exhibited significantly improved seed germination and seedling vigor compared with the un-inoculated seeds. The bacterial inoculation significantly increased root biomass, straw yield, grain yield, chlorophyll and carotenoid in the rice plant. Moreover, As uptake from root to shoot and As accumulation in straw and grain decreased significantly as a result of the bacterial inoculation. Noteworthy, the inoculation effect is more prominent in non-flooded soil than it is in flooded soil. Owing to its wide action spectrum, this As(III)-oxidizing PGPB could serve as a potential bio-inoculant for mitigation of As in paddies and sustainable rice production in As-contaminated areas.
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http://dx.doi.org/10.1016/j.jhazmat.2015.09.044DOI Listing
January 2016

Depth-resolved abundance and diversity of arsenite-oxidizing bacteria in the groundwater of Beimen, a blackfoot disease endemic area of southwestern Taiwan.

Water Res 2013 Dec 20;47(19):6983-91. Epub 2013 Oct 20.

Department of Earth Sciences, National Cheng Kung University, Tainan 70101, Taiwan.

The role of arsenite oxidizers in natural attenuation of arsenic pollution necessitates studies on their abundance and diversity in arsenic-contaminated aquifers. In this study, most probable number-polymerase chain reaction (MPN-PCR) and denaturing gradient gel electrophoresis (DGGE) was applied to monitor depth-wise abundance and diversity of aerobic arsenite oxidizers in arsenic-enriched groundwater of Beimen, southwestern Taiwan. The results revealed that the abundance of arsenite oxidizers ranged from 0.04 to 0.22, and the lowest ratio was observed in the most arsenic-enriched and comparatively more reduced groundwater (depth 200 m) of Beimen 1. The highest ratio was observed in the less arsenic-enriched and less reduced groundwater (depth 60 m) of Beimen 2B. DGGE profiles showed a shift in diversity of arsenite oxidizers, consisting of members of the Betaproteobacteria (61%), Alphaproteobacteria (28%) and Gammaproteobacteria (11%), depending on mainly arsenic concentration and redox level in groundwater. Groundwater with the lowest arsenic and highest dissolved oxygen at Beimen 2B harbored 78% of the arsenite oxidizers communities, while groundwater with the highest arsenic and lowest dissolved oxygen at Beimen 1 and Beimen-Jinhu harbored 17 and 22% of arsenite oxidizers communities, respectively. Pseudomonas sp. was found only in groundwater containing high arsenic at Beimen 1 and Beimen-Jinhu, while arsenite oxidizers belonging to Alpha- and Betaproteobacteria were dominated in groundwater containing low arsenic.
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http://dx.doi.org/10.1016/j.watres.2013.07.049DOI Listing
December 2013

Molecular fingerprinting of bacterial communities in enriched azo dye (Reactive Violet 5R) decolorising native acclimatised bacterial consortia.

Bioresour Technol 2013 Aug 22;142:436-44. Epub 2013 May 22.

Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390 002, Gujarat, India.

Reactive Violet 5R (RV5R) decolorising acclimatised bacterial consortia were enriched from industrial effluent contaminated and pristine samples from Gujarat, India on several different media. Twelve acclimatised consortia were selected for the study which were able to decolorise 100mg/L RV5R in 30 h under shaking or static conditions. Eubacterial diversity was studied by 16S rRNA gene based culture-independent methods, using HaeIII and Hinf1 enzymes for ARDRA and V3 region based DGGE analysis, forming total 6 clusters in both analysis. Decolorised end products of all the consortia were analysed by FTIR showing cleavage of the azo bond and group modifications. GC-MS data of dye decolorised end products of Gly consortium obtained from hydrocarbon contaminated soil demonstrated benzene ring cleavage activity. Present study suggests that enrichment of acclimatised consortia under different conditions can result in diverse microbial communities that differentially degrade RV5R and can provide rich source of dye decolorising strains.
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http://dx.doi.org/10.1016/j.biortech.2013.05.057DOI Listing
August 2013