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  • Closed Access
    Authors: 
    Norberto Castillo; Russell J. Boyd;
    Publisher: Elsevier BV

    Abstract We report a study of the inclusion complex of p-chlorophenol inside α-cyclodextrin (α-CD) by the theory of atoms in molecules (AIM). We use a quantitative comparison of some AIM properties of isolated p-chlorophenol (PCP) and the inclusion complex (PCP-CD) and we characterize some weak interactions within the host–guest complex. Furthermore, we compare the electrophilic aromatic substitution on the p-chlorophenol in the isolated state and inside α-CD. The analysis of the bond critical points of PCP shows that there is no trend in the effect on the AIM properties of PCP due to inclusion in the α-CD.

  • Open Access
    Authors: 
    Xue Xu; Yuan Zhou; Xiaowen Feng; Xiong Li; Mohammad Asad; Derek Li; Bo Liao; Jianqiang Li; Qinghua Cui; Edwin Wang;
    Publisher: American Association for the Advancement of Science (AAAS)
    Project: NSERC

    There is an ongoing debate on the importance of genetic factors in cancer development, where gene-centered cancer predisposition seems to show that only 5 to 10% of the cancer cases are inheritable. By conducting a systematic analysis of germline genomes of 9712 cancer patients representing 22 common cancer types along with 16,670 noncancer individuals, we identified seven cancer-associated germline genomic patterns (CGGPs), which summarized trinucleotide mutational spectra of germline genomes. A few CGGPs were consistently enriched in the germline genomes of patients whose tumors had smoking signatures or correlated with oncogenesis- and genome instability–related mutations. Furthermore, subgroups defined by the CGGPs were significantly associated with distinct oncogenic pathways, tumor histological subtypes, and prognosis in 13 common cancer types, suggesting that germline genomic patterns enable to inform treatment and clinical outcomes. These results provided evidence that cancer risk and clinical outcomes could be encoded in germline genomes. Germline variants when organized as genomic patterns are associated with cancer risk, oncogenic pathways, and clinical outcomes.

  • Closed Access
    Authors: 
    Kelli E. King; James J. McCormick; Melissa D. Côté; Morgan K. McManus; Serena Topshee; Glen P. Kenny;
    Publisher: Wiley
  • Authors: 
    J.A. Heddle; J.D. Gingerich;
    Publisher: Elsevier
  • Publication . Conference object . 2021
    Authors: 
    Tuofu Li; Javin Jia Liu; Yintao Tai; Yuxuan Tian;
    Publisher: SPIE

    Brain tumors are a hazardous type of tumor, and they build pressure inside the skull when they grow, which can potentially cause brain damage or even death. Attention mechanisms are widely adopted in state-of-the-art deep learning architectures for computer vision and neural translation tasks since they enhance networks' ability to capture spatial and channel-wise relationships. We offer an attention-based image segmentation model that outlines the brain tumors in Magnetic Resonance Imaging (MRI) scans if present. In the paper, we mainly focus on integrating Squeeze-and-Excitation Block and CBAM into the commonly used segmentation model, U-Net, to resolve the problem of concatenating unnecessary information into the decoder blocks and attempt to locate the tumor boundaries. Our research clearly shows the application of the attention mechanism in U-Net, incorporates the Squeeze-and-Excitation with CBAM, and improves the performance in the brain tumor segmentation task. The model is delivered on an app with additional text to speech and chatbot features provided.

  • Closed Access
    Authors: 
    Na Kong; Hongbin Li;
    Publisher: Wiley

    Due to their potential biomedical applications, protein-based hydrogels have attracted considerable interest. Although various methods have been developed to engineer self-assembling, physically-crosslinked protein hydrogels, exploring novel driving forces to engineer such hydrogels remains challenging. Protein fragment reconstitution, also known as fragment complementation, is a self-assembling mechanism by which protein fragments can reconstitute the folded conformation of the native protein when split into two halves. Although it has been used in biophysical studies and bioassays, fragment reconstitution has not been explored for hydrogel construction. Using a small protein GL5 as a model, which is capable of fragment reconstitution to reconstitute the folded GL5 spontaneously when split into two halves, GN and GC, we demonstrate that protein fragment reconstitution is a novel driving force for engineering self-assembling reversible protein hydrogels. Fragment reconstitution between GN and GC crosslinks GN and GC-containing proteins into self-assembling reversible protein hydrogels. These novel hydrogels show temperature-dependent reversible sol-gel transition, and excellent property against erosion in water. Since many proteins can undergo fragment reconstitution, we anticipate that such fragment reconstitution may offer a general driving force for engineering protein hydrogels from a variety of proteins, and thus significantly expanding the ‘toolbox’ currently available in the field of biomaterials.

  • Authors: 
    Dean H. Gatzlaff; Cynthia Holmes;
    Publisher: Elsevier BV

    This study examines the feasibility of constructing reliable commercial property price indices using property tax records. We employ the Clapp and Giacotto (1992) assessed-value method to estimate price indices from 1988:4 to 2008:4 for commercial properties in Florida. The estimated Florida commercial property price index is compared to the Moody’s/REAL Commercial Property Price Index (CPPI) and to the transaction-based index (TBI) produced by the Commercial Real Estate Data Lab at MIT. Our results are promising, suggesting that this widely-available data source can be used to produce commercial price indices for a wide variety of precise market locations and specific investor segments on an ongoing basis. We use our comprehensive database to examine two specific subsets in more detail. First, we narrow our range to focus on just the office sector for Florida. We compare price movements for the Florida office sector with the comparable CPPI. Estimates produce very similar price movements providing support to both methods. Second, we contrast the price performance of higher- and lower-valued properties. Chow tests indicate that Florida commercial properties assessed at $2.5 million, or above, appreciated on average at greater rates than those assessed below $2.5 million. In addition, our estimates indicate that highervalued properties performed especially well during periods of economic expansion. This finding represents an important contribution toward understanding the relative performance of smaller and institutional-grade commercial properties.

  • Closed Access
    Authors: 
    Alidad Amirfazli; Alireza Keshavarz; L Zhang; A. W. Neumann;
    Publisher: Elsevier BV

    Contact angle measurements for three n-alkanes, heptane, octane, and nonane, on two different self-assembled surfaces (SAM) are reported as a function of drop size. These liquids all formed low contact angles (below 20 degrees ); the measurements were performed using an accurate method for systems with low contact angle, ADSA-D. The observed drop size dependence of the contact angles was interpreted using the modified Young equation. It was concluded that the observed drop size dependence of contact angles was due to line tension. The choice of systems also provided the opportunity to examine the behavior of the line tension for systems near wetting (i.e., low contact angles). It was determined that the line tension is positive and ranges from below 10(-7) to just below 10(-6) J/m for the systems studied; the observations suggested that the line tension decreases as the contact angle decreases and likely vanishes at complete wetting.

  • Publication . Part of book or chapter of book . 2016
    Closed Access
    Authors: 
    Jake Cosme; Irina Tchernyshyov; Anthony O. Gramolini;
    Publisher: Springer International Publishing

    Mass spectrometry (MS) has provided some paradigm-shifting technology to the field of cardiac biology. Recent advances in MS have made protein identification into a high throughput analytic tool and improved accuracy and sensitivity of protein quantitation. Many of the tools available to scientists trying to answer fundamental questions of basic heart function and mechanisms of disease are quite robust and versatile. MS-based cardiac proteomic approaches have developed to such an extent that a researcher can design experiments to answer clear hypotheses, but also studies can also be ‘hypothesis-generating’, ultimately leading to deeper analyses and considerations. Here, we will outline the basic concepts of MS in an effort to explain the potential of this technology in investigating cardiac based research questions. Principles of how current instrumentation functions and how data is acquired will be introduced. Protein quantitation in MS is available in many varieties and applications; this chapter will outline current available technologies in protein quantitation such as isotope-labeled and label-free approaches. With the introductory knowledge of MS and protein quantitation, we will examine some key cardiac proteomics studies and discuss how these principles have been applied to answer specific research questions.

  • Closed Access
    Authors: 
    Raoul J. Mutter; Andrew G. Neuman;
    Publisher: Geological Society of London
Include:
3,046,394 Research products, page 3 of 304,640
  • Closed Access
    Authors: 
    Norberto Castillo; Russell J. Boyd;
    Publisher: Elsevier BV

    Abstract We report a study of the inclusion complex of p-chlorophenol inside α-cyclodextrin (α-CD) by the theory of atoms in molecules (AIM). We use a quantitative comparison of some AIM properties of isolated p-chlorophenol (PCP) and the inclusion complex (PCP-CD) and we characterize some weak interactions within the host–guest complex. Furthermore, we compare the electrophilic aromatic substitution on the p-chlorophenol in the isolated state and inside α-CD. The analysis of the bond critical points of PCP shows that there is no trend in the effect on the AIM properties of PCP due to inclusion in the α-CD.

  • Open Access
    Authors: 
    Xue Xu; Yuan Zhou; Xiaowen Feng; Xiong Li; Mohammad Asad; Derek Li; Bo Liao; Jianqiang Li; Qinghua Cui; Edwin Wang;
    Publisher: American Association for the Advancement of Science (AAAS)
    Project: NSERC

    There is an ongoing debate on the importance of genetic factors in cancer development, where gene-centered cancer predisposition seems to show that only 5 to 10% of the cancer cases are inheritable. By conducting a systematic analysis of germline genomes of 9712 cancer patients representing 22 common cancer types along with 16,670 noncancer individuals, we identified seven cancer-associated germline genomic patterns (CGGPs), which summarized trinucleotide mutational spectra of germline genomes. A few CGGPs were consistently enriched in the germline genomes of patients whose tumors had smoking signatures or correlated with oncogenesis- and genome instability–related mutations. Furthermore, subgroups defined by the CGGPs were significantly associated with distinct oncogenic pathways, tumor histological subtypes, and prognosis in 13 common cancer types, suggesting that germline genomic patterns enable to inform treatment and clinical outcomes. These results provided evidence that cancer risk and clinical outcomes could be encoded in germline genomes. Germline variants when organized as genomic patterns are associated with cancer risk, oncogenic pathways, and clinical outcomes.

  • Closed Access
    Authors: 
    Kelli E. King; James J. McCormick; Melissa D. Côté; Morgan K. McManus; Serena Topshee; Glen P. Kenny;
    Publisher: Wiley
  • Authors: 
    J.A. Heddle; J.D. Gingerich;
    Publisher: Elsevier
  • Publication . Conference object . 2021
    Authors: 
    Tuofu Li; Javin Jia Liu; Yintao Tai; Yuxuan Tian;
    Publisher: SPIE

    Brain tumors are a hazardous type of tumor, and they build pressure inside the skull when they grow, which can potentially cause brain damage or even death. Attention mechanisms are widely adopted in state-of-the-art deep learning architectures for computer vision and neural translation tasks since they enhance networks' ability to capture spatial and channel-wise relationships. We offer an attention-based image segmentation model that outlines the brain tumors in Magnetic Resonance Imaging (MRI) scans if present. In the paper, we mainly focus on integrating Squeeze-and-Excitation Block and CBAM into the commonly used segmentation model, U-Net, to resolve the problem of concatenating unnecessary information into the decoder blocks and attempt to locate the tumor boundaries. Our research clearly shows the application of the attention mechanism in U-Net, incorporates the Squeeze-and-Excitation with CBAM, and improves the performance in the brain tumor segmentation task. The model is delivered on an app with additional text to speech and chatbot features provided.

  • Closed Access
    Authors: 
    Na Kong; Hongbin Li;
    Publisher: Wiley

    Due to their potential biomedical applications, protein-based hydrogels have attracted considerable interest. Although various methods have been developed to engineer self-assembling, physically-crosslinked protein hydrogels, exploring novel driving forces to engineer such hydrogels remains challenging. Protein fragment reconstitution, also known as fragment complementation, is a self-assembling mechanism by which protein fragments can reconstitute the folded conformation of the native protein when split into two halves. Although it has been used in biophysical studies and bioassays, fragment reconstitution has not been explored for hydrogel construction. Using a small protein GL5 as a model, which is capable of fragment reconstitution to reconstitute the folded GL5 spontaneously when split into two halves, GN and GC, we demonstrate that protein fragment reconstitution is a novel driving force for engineering self-assembling reversible protein hydrogels. Fragment reconstitution between GN and GC crosslinks GN and GC-containing proteins into self-assembling reversible protein hydrogels. These novel hydrogels show temperature-dependent reversible sol-gel transition, and excellent property against erosion in water. Since many proteins can undergo fragment reconstitution, we anticipate that such fragment reconstitution may offer a general driving force for engineering protein hydrogels from a variety of proteins, and thus significantly expanding the ‘toolbox’ currently available in the field of biomaterials.

  • Authors: 
    Dean H. Gatzlaff; Cynthia Holmes;
    Publisher: Elsevier BV

    This study examines the feasibility of constructing reliable commercial property price indices using property tax records. We employ the Clapp and Giacotto (1992) assessed-value method to estimate price indices from 1988:4 to 2008:4 for commercial properties in Florida. The estimated Florida commercial property price index is compared to the Moody’s/REAL Commercial Property Price Index (CPPI) and to the transaction-based index (TBI) produced by the Commercial Real Estate Data Lab at MIT. Our results are promising, suggesting that this widely-available data source can be used to produce commercial price indices for a wide variety of precise market locations and specific investor segments on an ongoing basis. We use our comprehensive database to examine two specific subsets in more detail. First, we narrow our range to focus on just the office sector for Florida. We compare price movements for the Florida office sector with the comparable CPPI. Estimates produce very similar price movements providing support to both methods. Second, we contrast the price performance of higher- and lower-valued properties. Chow tests indicate that Florida commercial properties assessed at $2.5 million, or above, appreciated on average at greater rates than those assessed below $2.5 million. In addition, our estimates indicate that highervalued properties performed especially well during periods of economic expansion. This finding represents an important contribution toward understanding the relative performance of smaller and institutional-grade commercial properties.

  • Closed Access
    Authors: 
    Alidad Amirfazli; Alireza Keshavarz; L Zhang; A. W. Neumann;
    Publisher: Elsevier BV

    Contact angle measurements for three n-alkanes, heptane, octane, and nonane, on two different self-assembled surfaces (SAM) are reported as a function of drop size. These liquids all formed low contact angles (below 20 degrees ); the measurements were performed using an accurate method for systems with low contact angle, ADSA-D. The observed drop size dependence of the contact angles was interpreted using the modified Young equation. It was concluded that the observed drop size dependence of contact angles was due to line tension. The choice of systems also provided the opportunity to examine the behavior of the line tension for systems near wetting (i.e., low contact angles). It was determined that the line tension is positive and ranges from below 10(-7) to just below 10(-6) J/m for the systems studied; the observations suggested that the line tension decreases as the contact angle decreases and likely vanishes at complete wetting.

  • Publication . Part of book or chapter of book . 2016
    Closed Access
    Authors: 
    Jake Cosme; Irina Tchernyshyov; Anthony O. Gramolini;
    Publisher: Springer International Publishing

    Mass spectrometry (MS) has provided some paradigm-shifting technology to the field of cardiac biology. Recent advances in MS have made protein identification into a high throughput analytic tool and improved accuracy and sensitivity of protein quantitation. Many of the tools available to scientists trying to answer fundamental questions of basic heart function and mechanisms of disease are quite robust and versatile. MS-based cardiac proteomic approaches have developed to such an extent that a researcher can design experiments to answer clear hypotheses, but also studies can also be ‘hypothesis-generating’, ultimately leading to deeper analyses and considerations. Here, we will outline the basic concepts of MS in an effort to explain the potential of this technology in investigating cardiac based research questions. Principles of how current instrumentation functions and how data is acquired will be introduced. Protein quantitation in MS is available in many varieties and applications; this chapter will outline current available technologies in protein quantitation such as isotope-labeled and label-free approaches. With the introductory knowledge of MS and protein quantitation, we will examine some key cardiac proteomics studies and discuss how these principles have been applied to answer specific research questions.

  • Closed Access
    Authors: 
    Raoul J. Mutter; Andrew G. Neuman;
    Publisher: Geological Society of London