Matching Items (33)
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Description

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

ContributorsOberthuer, Dominik (Author) / Knoska, Juraj (Author) / Wiedorn, Max O. (Author) / Beyerlein, Kenneth R. (Author) / Bushnell, David A. (Author) / Kovaleva, Elena G. (Author) / Heymann, Michael (Author) / Gumprecht, Lars (Author) / Kirian, Richard (Author) / Barty, Anton (Author) / Mariani, Valerio (Author) / Tolstikova, Aleksandra (Author) / Adriano, Luigi (Author) / Awel, Salah (Author) / Barthelmess, Miriam (Author) / Dorner, Katerina (Author) / Xavier, P. Lourdu (Author) / Yefanov, Oleksandr (Author) / James, Daniel (Author) / Nelson, Garrett (Author) / Wang, Dingjie (Author) / Calvey, George (Author) / Chen, Yujie (Author) / Schmidt, Andrea (Author) / Szczepek, Michael (Author) / Frielingsdorf, Stefan (Author) / Lenz, Oliver (Author) / Snell, Edward (Author) / Robinson, Philip J. (Author) / Sarler, Bozidar (Author) / Belsak, Grega (Author) / Macek, Marjan (Author) / Wilde, Fabian (Author) / Aquila, Andrew (Author) / Boutet, Sebastien (Author) / Liang, Mengning (Author) / Hunter, Mark S. (Author) / Scheerer, Patrick (Author) / Lipscomb, John D. (Author) / Weierstall, Uwe (Author) / Kornberg, Roger D. (Author) / Spence, John (Author) / Pollack, Lois (Author) / Chapman, Henry N. (Author) / Bajt, Sasa (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor)
Created2017-03-16
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Description

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a

X-ray free-electron lasers provide novel opportunities to conduct single particle analysis on nanoscale particles. Coherent diffractive imaging experiments were performed at the Linac Coherent Light Source (LCLS), SLAC National Laboratory, exposing single inorganic core-shell nanoparticles to femtosecond hard-X-ray pulses. Each facetted nanoparticle consisted of a crystalline gold core and a differently shaped palladium shell. Scattered intensities were observed up to about 7 nm resolution. Analysis of the scattering patterns revealed the size distribution of the samples, which is consistent with that obtained from direct real-space imaging by electron microscopy. Scattering patterns resulting from single particles were selected and compiled into a dataset which can be valuable for algorithm developments in single particle scattering research.

ContributorsLi, Xuanxuan (Author) / Chiu, Chun-Ya (Author) / Wang, Hsiang-Ju (Author) / Kassemeyer, Stephan (Author) / Botha, Sabine (Author) / Shoeman, Robert L. (Author) / Lawrence, Robert (Author) / Kupitz, Christopher (Author) / Kirian, Richard (Author) / James, Daniel (Author) / Wang, Dingjie (Author) / Nelson, Garrett (Author) / Messerschmidt, Marc (Author) / Boutet, Sebastien (Author) / Williams, Garth J. (Author) / Hartman, Elisabeth (Author) / Jafarpour, Aliakbar (Author) / Foucar, Lutz M. (Author) / Barty, Anton (Author) / Chapman, Henry (Author) / Liang, Mengning (Author) / Menzel, Andreas (Author) / Wang, Fenglin (Author) / Basu, Shibom (Author) / Fromme, Raimund (Author) / Doak, R. Bruce (Author) / Fromme, Petra (Author) / Weierstall, Uwe (Author) / Huang, Michael H. (Author) / Spence, John (Author) / Schlichting, Ilme (Author) / Hogue, Brenda (Author) / Liu, Haiguang (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / School of Life Sciences (Contributor)
Created2017-04-11
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Description

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of

Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a well-characterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 μm diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 Ångström were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.

ContributorsMunke, Anna (Author) / Andreasson, Jakob (Author) / Aquila, Andrew (Author) / Awel, Salah (Author) / Ayyer, Kartik (Author) / Barty, Anton (Author) / Bean, Richard J. (Author) / Berntsen, Peter (Author) / Bielecki, Johan (Author) / Boutet, Sebastien (Author) / Bucher, Maximilian (Author) / Chapman, Henry N. (Author) / Daurer, Benedikt J. (Author) / DeMirci, Hasan (Author) / Elser, Veit (Author) / Fromme, Petra (Author) / Hajdu, Janos (Author) / Hantke, Max F. (Author) / Higashiura, Akifumi (Author) / Hogue, Brenda (Author) / Hosseinizadeh, Ahmad (Author) / Kim, Yoonhee (Author) / Kirian, Richard (Author) / Reddy, Hemanth K. N. (Author) / Lan, Ti-Yen (Author) / Larsson, Daniel S. D. (Author) / Liu, Haiguang (Author) / Loh, N. Duane (Author) / Maia, Filipe R. N. C. (Author) / Mancuso, Adrian P. (Author) / Muhlig, Kerstin (Author) / Nakagawa, Atsushi (Author) / Nam, Daewoong (Author) / Nelson, Garrett (Author) / Nettelblad, Carl (Author) / Okamoto, Kenta (Author) / Ourmazd, Abbas (Author) / Rose, Max (Author) / van der Schot, Gijs (Author) / Schwander, Peter (Author) / Seibert, M. Marvin (Author) / Sellberg, Jonas A. (Author) / Sierra, Raymond G. (Author) / Song, Changyong (Author) / Svenda, Martin (Author) / Timneanu, Nicusor (Author) / Vartanyants, Ivan A. (Author) / Westphal, Daniel (Author) / Wiedom, Max O. (Author) / Williams, Garth J. (Author) / Xavier, Paulraj Lourdu (Author) / Soon, Chun Hong (Author) / Zook, James (Author) / College of Liberal Arts and Sciences (Contributor, Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Life Sciences (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Department of Physics (Contributor)
Created2016-08-01
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Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement.

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
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Description
Objectives: Although childhood obesity has received growing attention, parents still fail to recognize overweight and obesity in their children. Accurate identification of overweight or obesity in their child is associated with the parent's responsiveness to interventions aimed at preventing weight-related health issues. Recent research shows that a child's age and

Objectives: Although childhood obesity has received growing attention, parents still fail to recognize overweight and obesity in their children. Accurate identification of overweight or obesity in their child is associated with the parent's responsiveness to interventions aimed at preventing weight-related health issues. Recent research shows that a child's age and gender are associated with parental misperception of their child's weight status, but little is known about the interaction of these factors across various age groups. This study examined the association between a wide range of parent, child, and household factors and the accuracy of parental perception of their child's body weight status compared to parent-measured body weight status. Methods: Data were collected from a random-digit-dial telephone survey of 1708 households located in five low-income New Jersey cities with large minority populations. A subset of 548 children whose parents completed the survey and returned a worksheet of parent-measured heights and weights were the focus of the analysis. Bivariate and multivariate analyses were performed to determine the factors significantly associated with parental perception of their child's body weight status. Results: Based on parent-measure heights and weights, 36% of the children were overweight or obese (OWOB). Only 21% of OWOB children were perceived by their parents as OWOB. Child gender, child body mass index (BMI) and parent BMI were significant independent predictors of parents' accuracy at perceiving their child's body weight status. Conclusion: Boys, OWOB children, and children of OWOB parents had significantly greater odds of parental underestimation of their body weight status. Parents had better recognition of OWOB in their daughters, especially older daughters, than in their sons, suggesting parental gender bias in identifying OWOB in children. Further research is needed regarding parental gender bias and its implications in OWOB identification in children.
ContributorsBader, Wendy (Author) / Ohri-Vachaspati, Punam (Thesis advisor) / Lloyd, Kristen (Committee member) / Crespo, Noe (Committee member) / Arizona State University (Publisher)
Created2013
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Description

Disparities in healthy food access are well documented in cross-sectional studies in communities across the United States. However, longitudinal studies examining changes in food environments within various neighborhood contexts are scarce. In a sample of 142 census tracts in four low-income, high-minority cities in New Jersey, United States, we examined

Disparities in healthy food access are well documented in cross-sectional studies in communities across the United States. However, longitudinal studies examining changes in food environments within various neighborhood contexts are scarce. In a sample of 142 census tracts in four low-income, high-minority cities in New Jersey, United States, we examined the availability of different types of food stores by census tract characteristics over time (2009–2017). Outlets were classified as supermarkets, small grocery stores, convenience stores, and pharmacies using multiple sources of data and a rigorous protocol. Census tracts were categorized by median household income and race/ethnicity of the population each year. Significant declines were observed in convenience store prevalence in lower- and medium-income and majority black tracts (p for trend: 0.004, 0.031, and 0.006 respectively), while a slight increase was observed in the prevalence of supermarkets in medium-income tracts (p for trend: 0.059). The decline in prevalence of convenience stores in lower-income and minority neighborhoods is likely attributable to declining incomes in these already poor communities. Compared to non-Hispanic neighborhoods, Hispanic communities had a higher prevalence of small groceries and convenience stores. This higher prevalence of smaller stores, coupled with shopping practices of Hispanic consumers, suggests that efforts to upgrade smaller stores in Hispanic communities may be more sustainable.

ContributorsOhri-Vachaspati, Punam (Author) / DeWeese, Robin (Author) / Acciai, Francesco (Author) / DeLia, Derek Michael, 1969- (Author) / Tulloch, David (Author) / Tong, Daoqin (Author) / Lorts, Cori (Author) / Yedidia, Michael J., 1946- (Author)
Created2019-07-03
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Description

In response to lack of access to healthy foods, many low-income communities are instituting local healthy corner store programs. Some stores also participate in the United States Department of Agriculture's Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) and the Supplemental Nutrition Assistance Program (SNAP). This study used

In response to lack of access to healthy foods, many low-income communities are instituting local healthy corner store programs. Some stores also participate in the United States Department of Agriculture's Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) and the Supplemental Nutrition Assistance Program (SNAP). This study used two assessment tools to compare the healthfulness of offerings at stores participating in local healthy store programs (upgraded stores), WIC, and/or SNAP to that of similar non-participating stores.

Based on store audits conducted in 315 New Jersey corner stores in 2014, we calculated healthy food availability scores using subsections of the Nutrition Environment Measures Survey for Corner Stores (NEMS-CS-Availability) and a short-form corner store audit tool (SCAT). We used multivariable regression to examine associations between program participation and scores on both instruments.

Adjusting for store and block group characteristics, stores participating in a local healthy store program had significantly higher SCAT scores than did non-participating stores (upgraded: M = 3.18, 95% CI 2.65–3.71; non-upgraded: M = 2.52, 95% CI 2.32–2.73); scores on the NEMS-CS-Availability did not differ (upgraded: M = 12.8, 95% CI 11.6–14.1; non-upgraded: M = 12.5, 95% CI 12.0–13.0). WIC-participating stores had significantly higher scores compared to non-participating stores on both tools. Stores participating in SNAP only (and not in WIC) scored significantly lower on both instruments compared to non-SNAP stores.

WIC-participating and non-SNAP corner stores had higher healthfulness scores on both assessment tools. Upgraded stores had higher healthfulness scores compared to non-upgraded stores on the SCAT.

ContributorsDeWeese, Robin (Author) / Todd, Michael (Author) / Karpyn, Allison (Author) / Yedidia, Michael J., 1946- (Author) / Kennedy, Michelle (Author) / Bruening, Meg (Author) / Wharton, Christopher M. (Author) / Ohri-Vachaspati, Punam (Author)
Created2016-06-29
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Description

Objective: The Social Ecological Model (SEM) has been used to describe the aetiology of childhood obesity and to develop a framework for prevention. The current paper applies the SEM to data collected at multiple levels, representing different layers of the SEM, and examines the unique and relative contribution of

Objective: The Social Ecological Model (SEM) has been used to describe the aetiology of childhood obesity and to develop a framework for prevention. The current paper applies the SEM to data collected at multiple levels, representing different layers of the SEM, and examines the unique and relative contribution of each layer to children's weight status.

Design: Cross-sectional survey of randomly selected households with children living in low-income diverse communities.

Setting: A telephone survey conducted in 2009-2010 collected information on parental perceptions of their neighbourhoods, and household, parent and child demographic characteristics. Parents provided measured height and weight data for their children. Geocoded data were used to calculate proximity of a child's residence to food and physical activity outlets.

Subjects: Analysis based on 560 children whose parents participated in the survey and provided measured heights and weights.

Results: Multiple logistic regression models were estimated to determine the joint contribution of elements within each layer of the SEM as well as the relative contribution of each layer. Layers of the SEM representing parental perceptions of their neighbourhoods, parent demographics and neighbourhood characteristics made the strongest contributions to predicting whether a child was overweight or obese. Layers of the SEM representing food and physical activity environments made smaller, but still significant, contributions to predicting children's weight status.

Conclusions: The approach used herein supports using the SEM for predicting child weight status and uncovers some of the most promising domains and strategies for childhood obesity prevention that can be used for designing interventions.

ContributorsOhri-Vachaspati, Punam (Author) / DeLia, Derek Michael, 1969- (Author) / DeWeese, Robin (Author) / Crespo, Noe C. (Author) / Todd, Michael (Author) / Yedidia, Michael J., 1946- (Author)
Created2014-11-06
Description

The New Jersey Childhood Obesity Study, funded by the Robert Wood Johnson Foundation, aims to provide vital information for planning, implementing and evaluating interventions aimed at preventing childhood obesity in five ew Jersey municipalities: Camden, Newark, New Brunswick, Trenton, and Vineland. These five communities are being supported by RWJF's New

The New Jersey Childhood Obesity Study, funded by the Robert Wood Johnson Foundation, aims to provide vital information for planning, implementing and evaluating interventions aimed at preventing childhood obesity in five ew Jersey municipalities: Camden, Newark, New Brunswick, Trenton, and Vineland. These five communities are being supported by RWJF's New Jersey Partnership for Healthy Kids program to plan and implement policy and environmental change strategies to prevent childhood obesity.

Effective interventions for addressing childhood obesity require community specific information on who is most at risk and on contributing factors that can be addressed through tailored interventions that meet the needs of the community.

Using a comprehensive research study, the Center for State Health Policy at Rutgers University is working collaboratively with the State Program Office for New Jersey Partnership for Healthy Kids and the five communities to address these information needs. The main components of the study include:

• A household survey of 1700 families with 3 -18 year old children

• De-identified heights and weights data from public school districts

• Assessment of the food and physical activity environments using objective data

Data books and maps based on the results of the study are being shared with the community coalitions in the five communities to help them plan their interventions.

Created2010
Description

The New Jersey Childhood Obesity Study, funded by the Robert Wood Johnson Foundation, aims to provide vital information for planning, implementing and evaluating interventions aimed at preventing childhood obesity in five New Jersey municipalities: Camden, Newark, New Brunswick, Trenton, and Vineland.

These five communities are being supported by RWJF's New Jersey

The New Jersey Childhood Obesity Study, funded by the Robert Wood Johnson Foundation, aims to provide vital information for planning, implementing and evaluating interventions aimed at preventing childhood obesity in five New Jersey municipalities: Camden, Newark, New Brunswick, Trenton, and Vineland.

These five communities are being supported by RWJF's New Jersey Partnership for Healthy Kids program to plan and implement policy and environmental change strategies to prevent childhood obesity.

Effective interventions for addressing childhood obesity require community-specific information on who is most at risk and on contributing factors that can be addressed through tailored interventions that meet the needs of the community.

Using a comprehensive research study, the Center for State Health Policy at Rutgers University is working collaboratively with the State Program Office for New Jersey Partnership for Healthy I<ids and the five communities to address these information needs. The main components of the study include:

• A household survey of 1700 families with 3 -18 year old children

• De-identified heights and weights data from public school districts

• Assessment of the food and physical activity environments using objective data

Data books and maps based on the results of the study are being shared with the community coalitions in the five communities to help them plan their interventions.

Created2010