Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project

Horvatovich, Pé,ter,Lundberg, Emma K.,Chen, Yu-Ju,Sung, Ting-Yi,He, Fuchu,Nice, Edouard C.,Goode, Robert J.,Yu, Simon,Ranganathan, Shoba,Baker, Mark S.,Domont, Gilberto B.,Velasquez, Erika,Li, D American Chemical Society 2015 Journal of Proteome Research Vol.14 No.9

<P>This paper summarizes the recent activities of the Chromosome-Centric Human Proteome Project (C-HPP) consortium, which develops new technologies to identify yet-to-be annotated proteins (termed “missing proteins”) in biological samples that lack sufficient experimental evidence at the protein level for confident protein identification. The C-HPP also aims to identify new protein forms that may be caused by genetic variability, post-translational modifications, and alternative splicing. Proteogenomic data integration forms the basis of the C-HPP’s activities; therefore, we have summarized some of the key approaches and their roles in the project. We present new analytical technologies that improve the chemical space and lower detection limits coupled to bioinformatics tools and some publicly available resources that can be used to improve data analysis or support the development of analytical assays. Most of this paper’s content has been compiled from posters, slides, and discussions presented in the series of C-HPP workshops held during 2014. All data (posters, presentations) used are available at the C-HPP Wiki (<uri xlink:href='http://c-hpp.webhosting.rug.nl/' xlink:type='simple'>http://c-hpp.webhosting.rug.nl/</uri>) and in the Supporting Information.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jprobs/2015/jprobs.2015.14.issue-9/pr5013009/production/images/medium/pr-2014-013009_0005.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/pr5013009'>ACS Electronic Supporting Info</A></P>

Comprehensive in vitro and in vivo risk assessments of b-lactam antibiotic and b-lactamase inhibitor loaded chitosan nanoparticles

Arianna J. Partow,Miju Kim,Peixin Fan,Ting Liu,Zhaohui Tong,Kwangcheol C. Jeong 한국공업화학회 2022 Journal of Industrial and Engineering Chemistry Vol.113 No.-

The safety of using nano-emulsion drug delivery systems is a growing concern. Here, we conducted riskassessments of an innovative combination therapy for multidrug resistant pathogens by encapsulatingcephalosporin antibiotics and b-lactamase inhibitors with chitosan nanoparticles (CNAIs) using in vitrohuman cell lines and an in vivo animal model, Caenorhabditis elegans. The four combinations of CNAIsincluding two cephalosporin antibiotics (cefotaxime and ceftiofur) with two b-lactamase inhibitors (tazobactamand clavulanate) were engineered as water–oil-water emulsions. CNAIs maintained stableantimicrobial activity in various thermal challenges. CNAIs exerted strong antimicrobial activity butdid not cause toxicity in human cell lines measured by cell membrane integrity, mitochondria activity,and reactive oxygen species generation. Reported damage was observed at 8 lg/mL and 16 lg/mL foronly two of the four combinations of CNAIs. More importantly, CNAIs at 4 lg/mL did not cause adverseeffects on the lifespan of C. elegans. In summary, CNAIs do not cause toxicity at working concentrationin vitro and in vivo risk assessments, suggesting that nano-emulsion drug delivery systems can be anew framework for developing treatments for multidrug pathogen infections.

Organic Thin‐Film Transistors: Simultaneous Modification of Bottom‐Contact Electrode and Dielectric Surfaces for Organic Thin‐Film Transistors Through Single‐Component Spin‐Cast Monolayers (Adv. Funct. Mater. 8/2011)

Acton, Orb,Dubey, Manish,Weidner, Tobias,O’Malley, Kevin M.,Kim, Tae‐,Wook,Ting, Guy G.,Hutchins, Daniel,Baio, J. E.,Lovejoy, Tracy C.,Gage, Alexander H.,Castner, David G.,Ma, Hong,Jen, Alex K.& WILEY‐VCH Verlag 2011 Advanced functional materials Vol.21 No.8

<P><B>Abstract</B></P><P>An efficient process is developed by spin‐coating a single‐component, self‐assembled monolayer (SAM) to simultaneously modify the bottom‐contact electrode and dielectric surfaces of organic thin‐film transistors (OTFTs). This effi cient interface modifi cation is achieved using <I>n</I>‐alkyl phosphonic acid based SAMs to prime silver bottom‐contacts and hafnium oxide (HfO<SUB>2</SUB>) dielectrics in low‐voltage OTFTs. Surface characterization using near edge X‐ray absorption fi ne structure (NEXAFS) spectroscopy, X‐ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared (ATR‐FTIR) spectroscopy, atomic force microscopy (AFM), and spectroscopic ellipsometry suggest this process yields structurally well‐defi ned phosphonate SAMs on both metal and oxide surfaces. Rational selection of the alkyl length of the SAM leads to greatly enhanced performance for both <I>n</I>‐channel (C<SUB>60</SUB>) and p‐channel (pentacene) based OTFTs. Specifi cally, SAMs of <I>n</I>‐octylphos‐phonic acid (OPA) provide both low‐contact resistance at the bottom‐contact electrodes and excellent interfacial properties for compact semiconductor grain growth with high carrier mobilities. OTFTs based on OPA modifi ed silver electrode/HfO<SUB>2</SUB> dielectric bottom‐contact structures can be operated using < 3V with low contact resistance (down to 700 Ohm‐cm), low subthreshold swing (as low as 75 mV dec<SUP>−1</SUP>), high on/off current ratios of 107, and charge carrier mobilities as high as 4.6 and 0.8 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP>, for C60 and pentacene, respectively. These results demonstrate that this is a simple and efficient process for improving the performance of bottom‐contact OTFTs.</P>

Optical characteristics of silver film on the moth-eye structure

C. J. Ting,H. Y. Tsai,C. P. Chou,H. Y. Lin,T. C. Wu 대한기계학회 2007 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.21 No.10

Cyst-Like Osteolytic Formations in Recombinant Human Bone Morphogenetic Protein-2 (rhBMP-2) Augmented Sheep Spinal Fusion

Pan, H.C.,Lee, S.,Ting, K.,Shen, J.,Wang, C.,Nguyen, A.,Berthiaume, E.A.,Zara, J.N.,Turner, A.S.,Seim, H.B.,Kwak, J.H.,Zhang, X.,Soo, C. American Association of Pathologists and Bacteriol 2017 The American journal of pathology Vol.187 No.7

<P>Multiple case reports using recombinant human bone morphogenetic protein-2 (rhBMP-2) have reported complications. However, the local adverse effects of rhBMP-2 application are not well documented. In this report we show that, in addition to promoting Lumbar spinal fusion through potent osteogenic effects, rhBMP-2 augmentation promotes local cyst-like osteolytic formations in sheep trabecular bones that have undergone anterior lumbar interbody fusion. Three months after operation, conventional computed tomography showed that the trabecular bones of the rhBMP-2 application groups could fuse, whereas no fusion was observed in the control group. Micro computed tomography analysis revealed that the core implant area's bone volume fraction and bone mineral density increased proportionately with rhBMP-2 dose. Multiple cyst-Like bone voids were observed in peri-implant areas when using rhBMP2 applications, and these sites showed significant bone mineral density decreases in relation to the unaffected regions. Biomechanically, these areas decreased in strength by 32% in comparison with noncystic areas. Histologically, rhBMP-2 affected void sites had an increased amount of fatty marrow, thinner trabecular bones, and significantly more adiponectin- and cathepsin K-positive cells. Despite promoting successful fusion, rhBMP-2 use in clinical applications may result in local adverse structural alterations and compromised biomechanical changes to the bone.</P>

Ginsenoside Rb1 Inhibits Cell Activation and Liver Fibrosis in Rat Hepatic Stellate Cells

Yu-Ting Lo,Ya-Hui Tsai,Shu-Ju Wu,Jiun-Rong Chen,C.-J. Chao 한국식품영양과학회 2011 Journal of medicinal food Vol.14 No.10

Chronic hepatitis/cirrhosis is the eighth leading cause of death in Taiwan. Excess accumulated extracellular matrix produced by activated hepatic stellate cells (HSCs) is the major cause of liver fibrosis. Ginsenoside Rb1, the most active compound purified from ginseng, has been considered to be hepatoprotective. This study investigated the effects of ginsenoside Rb1 (98.8% purity) on activation, proliferation, and profibrotic factors in rat HSC-T6 cells under H₂O₂oxidative stress. Rat HSC-T6 cells were activated by 10 nM H₂O₂and then incubated with different concentrations of ginsenoside Rb1 (5, 10, 20, 40, and 80 μg/mL) for 24 hours. Medium containing 0.08% dimethyl sulfoxide or 5 mM N-acetyl-l-cysteine was used as a negative or positive control, respectively. The results showed that ginsenoside Rb1 at 5–40 μg/mL significantly reduced α-smooth muscle actin levels and at 5–80 μg/mL inhibited cell proliferation in HSC-T6 cells after induction with H₂O₂(P<.05). Collagen secreted by HSC-T6 cells was decreased by ginsenoside Rb1 at 5–80 μg/mL (P<.05). Protein expression of transforming growth factor-β1 (TGF-β1), matrix metalloproteinase (MMP)-2, and tissue inhibitor of metalloproteinase (TIMP)-1 was suppressed by ginsenoside Rb1 at 10–80 μg/mL (P<.05). In addition, mRNA expression of type I and III collagen, TGF-β1, and TIMP-1 was inhibited by ginsenoside Rb1 (10 and 80 μg/mL) (P<.05). Therefore, ginsenoside Rb1 exerted an antifibrotic effect on HSCs by inhibiting activation, proliferation, and expression of collagen, TGF-β1, MMP-2, and TIMP-1.

Association of Condylar Bone Quality with TMJ Osteoarthritis

Shi, J.,Lee, S.,Pan, H. C.,Mohammad, A.,Lin, A.,Guo, W.,Chen, E.,Ahn, A.,Li, J.,Ting, K. Journal of Dental Research, Inc 2017 Journal of dental research Vol.96 No.8

<P>The etiology and treatment of temporomandibular joint (TMJ) osteoarthritis (TMJOA) remain complex and unclear. Based on clinical observations, we hypothesized that low condylar bone quality is significantly correlated with TMJOA and explored this association in a cross-sectional study with human patients. A total of 254 postmenopausal female participants were included in this study. Radiographic findings from cone beam computed tomography (CBCT) and clinical symptoms were used to classify each TMJ data sample as healthy control (n = 124) or TMJOA (n = 130). Condylar bone mineral density (BMD) (computed tomography Hounsfield unit [CT HU]) and bone volume fraction (BV/TV) were measured and modeled as predictors of healthy control versus TMJOA status in multilevel logistic regression analyses. Both CT HU (adjusted odds ratio [AOR] = 0.9989, interquartile odds ratio [IOR] = 0.4206) and BV/TV (AOR= 0.8096, IOR = 0.1769) were negatively associated with TMJOA (P = 0.049, 0.011, respectively). To assess the diagnostic performance of CT HU and BV/TV for identification of TMJOA, receiver operating characteristic (ROC) curves were plotted. The estimated areas under the curve (AUC) were 0.6622 for BV/TV alone, 0.6074 for CT HU alone, and 0.7136 for CT HU and BV/TV together. The model incorporating CT HU and BV/TV together had a significantly higher AUC than the models using BV/TV alone (P = 0.038) or HU alone (P = 0.021). In conclusion, we found that low condylar bone quality was significantly correlated with TMJOA development and that condylar CT HU and BV/TV can be used together as a potential diagnostic tool for TMJOA. Careful clinical evaluation of the condyle coupled with appropriate radiographic interpretation would thus be critical for the early detection of TMJOA.</P>

Systems Studies and Modeling of Advanced Life Support Systems

Kang, S.,Ting, K. C.,Both, A. J. 한국농업기계학회 2001 Agricultural and Biosystems Engineering Vol.2 No.2

Advanced Life Support Systems (ALSS) are being studied to support human lift during long-duration space missions. ALSS can be categorized into four subsystems: Crew, Biomass Production, Food Processing and Nutrition, Waste Processing and Resource Recovery. The System Studies and Modeling (SSM) team of New Jersey-NASA Specialized Center of Research and Training (NJ-NSCORT) has facilitated and conducted analyses of ALSS to address systems level issues. The underlying concept of the SSM work is to enable the effective utilization of information to aid in planning, analysis, design, management, and operation of ALSS and their components. Analytical tools and computer models for ALSS analyses have been developed and implemented for value-added information processing. The results of analyses have been delivered through the internet for effective communication within the advanced life support (ALS) community. Several modeling paradigms have been explored by developing tools for use in systems analysis. They include object-oriented approach for top-level models, procedural approach for process-level models, and application of commercially available modeling tools such as MATLAB®/Simulink®. Every paradigm has its particular applicability for the purpose of modeling work. An overview is presented of the systems studies and modeling work conducted by the NJ-NSCORT SSM team in its efforts to provide systems analysis capabilities to the ALS community. The experience gained and the analytical tools developed from this work can be extended to solving problems encountered in general agriculture.

Session 8 B CONTROLLED PLANT PRODUCTION SYSTEM & FACILITIES ( 1 ) : Systems Studies and Modeling of Advanced Life Support System

(S. Kang),(K. C. Ting),(A. J. Both) 한국농업기계학회 2000 Agricultural Mechanization in Korea Vol.3 No.15

Physical Activity and Quality of Life

Diane L. Gill,Cara C. Hammond,Erin J. Reifsteck,Christine M. Jehu,Rennae A. Williams,Melanie M. Adams,Elizabeth H. Lange,Katie Becofsky,Enid Rodriguez,Ya-Ting Shang 대한예방의학회 2013 Journal of Preventive Medicine and Public Health Vol.46 No.suppl

Physical activity (PA) professionals and participants recognize enhanced quality of life (QoL) as a benefit of and motivator for PA. However, QoL measures are often problematic and rarely consider the participants’ perspective. This paper focuses on recent findings from a larger project on the role of QoL in PA and health promotion. More specifically, we focus on the views of participants and potential participants to better understand the relationship of PA and QoL. In earlier stages of the project we began with a conceptual model of QoL and developed a survey. We now focus on participants’ views and ask two questions: 1) what is QoL? and 2) how does PA relate to QoL? We first asked those questions of a large sample of university students and community participants as open-ended survey items, and then asked focus groups of community participants. Overall, participants’ responses reflected the multidimensional, integrative QoL model, but the responses and patterns provided information that may not be picked up with typical survey measures. Findings suggest that PA contributes to multiple aspects of QoL, that social and emotional benefits are primary motivators and outcomes for participants, and that the meaning of QoL and PA benefits is subjective and contextualized, varying across individuals and settings. Programs that directly target and highlight the multiple dimensions and integrative QoL, while considering the individual participants and contexts, may enhance both PA motivation and participants’ health and QoL.