1,104 research outputs found
Three novel F8 mutations in sporadic haemophilia A cases
No full textLetter to the editorRashid Hussain, Noman Bin Abid, Sajjad Hussain, Zeeshan Shaukat, Mudassir Altaf, Sara Altaf, and Gulzar Niaz
XSEDE Enabling Function Use Cases, version 2.0
No full textThese are the “enabling functions” provided by the XSEDE system architecture. They are the common ingredients that enable XSEDE to satisfy the use cases in every other category. Each public research computing community has its own enabling use cases: some that overlap with XSEDE’s, others that are distinct characteristics of the community.
The purpose of enabling functions is to provide a common set of system-wide features that can be used when satisfying other use cases. Enabling functions arise from reviewing a large set of use cases from different types of community members and identifying the common features they share. For example, most use cases—whether from High-Performance Computing, Data Management, Campus Bridging, or Science Gateways—assume there’s a community-wide “login” feature that allows individuals to register, obtain credentials, and then use those credentials to login. Rather than design a custom login feature for every use case, we instead define an enabling function and assume most, if not all, use cases will use it.
XSEDE maintains descriptions of our enabling functions for several reasons. First, they support the introduction of new services from community members and partners by identifying features that must be carefully integrated in order to provide a smooth experience for XSEDE community members. Second, these descriptions allow XSEDE to consider new and better ways to provide each enabling function without unintentionally losing important features in the process. Finally, they support partnership and transition discussions by providing a basis for comparison with other systems.
Each of these enabling functions, with the exception of CAN-05, was originally written as an individual document during the XSEDE-1 project between 2012 and 2015 using a more technical format and terminology. These previous versions are linked in the References section.Open Restriction set for Item 111795 on 2019-08-13T23:57:18Z with date null by [email protected] by Lee Liming ([email protected]) on 2019-08-14T00:11:51Z
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Previous issue date: 2019-08-13National Science Foundation OCI-1053575Ope
XSEDE Enabling Function Use Cases, version 2.0
No full textThese are the “enabling functions” provided by the XSEDE system architecture. They are the common ingredients that enable XSEDE to satisfy the use cases in every other category. Each public research computing community has its own enabling use cases: some that overlap with XSEDE’s, others that are distinct characteristics of the community.
The purpose of enabling functions is to provide a common set of system-wide features that can be used when satisfying other use cases. Enabling functions arise from reviewing a large set of use cases from different types of community members and identifying the common features they share. For example, most use cases—whether from High-Performance Computing, Data Management, Campus Bridging, or Science Gateways—assume there’s a community-wide “login” feature that allows individuals to register, obtain credentials, and then use those credentials to login. Rather than design a custom login feature for every use case, we instead define an enabling function and assume most, if not all, use cases will use it.
XSEDE maintains descriptions of our enabling functions for several reasons. First, they support the introduction of new services from community members and partners by identifying features that must be carefully integrated in order to provide a smooth experience for XSEDE community members. Second, these descriptions allow XSEDE to consider new and better ways to provide each enabling function without unintentionally losing important features in the process. Finally, they support partnership and transition discussions by providing a basis for comparison with other systems.
Each of these enabling functions, with the exception of CAN-05, was originally written as an individual document during the XSEDE-1 project between 2012 and 2015 using a more technical format and terminology. These previous versions are linked in the References section.National Science Foundation OCI-1053575Ope
Emphasizing brand heritage: does it work? And how?
No full textAbstract not availableGregory M. Rose, Altaf Merchant, Ulrich R. Orth, Florian Horstman
CARBON EXCHANGE IN A TEMPERATE DECIDUOUS FOREST IN SOUTHERN ONTARIO
No full textContinuous measurements of carbon fluxes and meteorological variables were made at a newly initiated flux tower site at an oak-dominant temperate deciduous forest in Southern Ontario, Canada from January to December 2012. Results indicate this forest was a moderate carbon sink in 2012. Annual values of net ecosystem productivity (NEP), gross ecosystem productivity (GEP) and ecosystem respiration (R) were 263 ± 30, 1192 and 922 g C m-2, respectively. An unusual warm period in March caused a strong increase in R. Erratic peaks of daily air temperature in April also increased R. A drought in July and early August reduced NEP rates when soil moisture values reached the lowest point of the year in late July and early August (minimum 0.023 m3 m-3). This decrease in NEP was mostly caused by a decrease in GEP, rather than increased R. Water use efficiency at this deciduous forest was 2.86 g C kg-1 H2O, indicating conservative water use by the forest. Downwelling photosynthetic active radiation (PAR) was a dominant environmental control on photosynthesis, followed by air temperature and vapour pressure deficit, except in extreme dry periods when soil water stress affected carbon uptake. Extremely cloudy days in the growing season resulted in net carbon release due to low photosynthetic uptake values. Results indicate that large climatic fluctuations in this region may cause high instability in photosynthetic carbon uptake and release from soil carbon pools. This study helps to evaluate and quantify the responses of deciduous forests in the Great Lakes region to future climate change and extreme weather events.Master of Science (MSc
Revealing intra-annual carbon sequestration patterns through xylem anatomy and eddy covariance fluxes in eastern white pine
No full textForests are major terrestrial carbon sinks, playing a crucial role in climate change mitigation. Nonetheless, the long-term seasonal carbon sequestration dynamics are scarcely understood. Here, we investigated the relationships between climate variability, carbon fluxes, and the xylem biomass in an 80-year-old plantation of Pinus strobus in Ontario, Canada. From Eddy Covariance tower, we obtained daily Gross Primary Production (GPP), precipitation, VPD and air temperature for the period 2003-2018. To estimate inter-and intra-annual xylem biomass accumulation we selected 12 trees and built wood anatomical chronologies of cell number (CN), cell wall area (CWA) and overall wall area per ring (RWA). We used moving windows correlations of daily climate data and GPP with anatomical chronologies to analyse their associations at intra-annual scale.
Temperature in early spring and precipitation in mid-spring and summer strongly positively affected GPP, while summer VPD had a negative effect. For the first time, we observed strong positive correlations between GPP in the growing season and CWA (proxy for carbon quantity in each xylem cell) both in earlywood (May 10 – Aug 1, r = 0.652) and latewood (Jul 3 – Sep 3, r = 0.885). Strong positive correlations were also found between GPP and CN and RWA (r ≥ 0.724). Our results suggest a direct influence of CO2 fluxes on the accumulation of carbon in woody biomass. This work will help to reduce uncertainties in woody carbon accumulation dynamics, opening new perspectives in the study of forest carbon cycle
A Study of Reduced Order 4D-VAR with a Finite Element Shallow Water Model
No full textForecast models often depend on unknown parameters, such as model initial and boundary conditions, or other tunable parameters not necessarily having any physical meaning. Calibration of these parameters to minimize errors between forecasted and observed states is called data assimilation. A common approach in this context are variational methods, of which four dimensional data variation (4D-VAR) is studied in this thesis. In 4D-VAR, a cost function is defined that penalizes misfits between observations and the corresponding numerical model results, obtained by running the model with the chosen configuration. Performing optimization with regard to this cost function yields an improved initial parameter set. Associated with this type of methods, however, are difficulties in connection with programming the adjoint model, which is needed to compute the exact gradient of the cost function. Additionally, having to integrate the adjoint model backwards in time adds significantly to the computational cost of the data assimilation process. To avoid manual implementation of adjoint code and to reduce computational complexity, approximation of the gradient calculation is considered through the use of proper orthogonal decomposition (POD), a flexible data-driven order reduction method. To facilitate this, a finite element model of the shallow water equations is tested with both the full adjoint 4D-VAR method and two different POD-reduced approaches. Twin experiments are performed and comparisons are made in terms of accuracy, computational complexity and sensitivity to perturbation and number of observation points.Applied mathematicsElectrical Engineering, Mathematics and Computer Scienc
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Slot Blot Assay for Detection of R Loops
No full textR loops (DNA-RNA hybrid) are three-stranded nucleic acid structures that comprise of template DNA strand hybridized with the nascent RNA leaving the displaced non-template strand. Although a programmed R loop formation can serve as powerful regulators of gene expression, these structures can also turn into major sources of genomic instability and contribute to the development of diseases. Therefore, understanding how cells prevent the deleterious consequences of R loops yet allow R loop formation to participate in various physiological processes will help to understand how their homeostasis is maintained. Detection and quantitative measurements of R loops are critical that largely relied on S9.6 antibody. Immunofluorescence methods are frequently used to localize and quantify R loops in the cell but they require specialized tools for analysis and relatively expensive; therefore, they are not always useful for initial assessments of R loop accumulation. Here, we describe an improved slot blot protocol to detect and estimate R loops and show its sensitivity and specificity using the S9.6 antibody. Since specific factors protecting cells from harmful R loop accumulation are expanding, this protocol can be used to determine R loop accumulation in research and clinical settings
Long-term eddy covariance fluxes and xylem anatomy for understanding carbon fixation in white pine woody biomass
No full textImproving our understanding of the carbon cycle is key to addressing the challenges of climate change. In this study, we investigated the relationships between intra and inter-annual climate variations, carbon fluxes, and the xylem biomass in an 80-year plantation of Pinus strobus at Turkey Point, Ontario, Canada. From eddy covariance tower, we obtained daily Gross Primary Production (GPP), precipitation and air temperature for the period 2003-2018. To determine inter-and intra-annual xylem biomass we selected 12 trees and built wood anatomical trait chronologies (cell lumen area, cell wall thickness, cell number, cell wall area and ring wall area) over the past 50 years. Using moving windows, we correlated all chronologies with daily climate data and GPP to analyse their associations at intra-annual scale.
The analysis showed that cell lumen area and cell wall thickness were strongly influenced by spring and summer temperature and precipitation. For the first time, we observed strong positive and significant correlations between GPP in the growing season and the cell wall area (which estimates the amount of carbon in each xylem cell) both in earlywood (May 10 - Aug 4, r = 0.685) and latewood (Jul 3 – Sep 3, r = 0.885). Strong positive correlations were also found between GPP and cell number and ring wall area. These results suggest a direct linkage between CO2 fluxes and the accumulation of carbon in woody biomass. This work will help to reconcile two important techniques that are widely used to study carbon sequestration in forests. It will help to reduce uncertainty in woody carbon accumulation and will open new perspectives in the study of the forest carbon cycle
State of the art: museum additions and their impact on occupant experience
No full textThis dissertation takes a critical look at the effects of art museum additions on occupants by addressing key questions: How does museum addition design affect visitors’ and museum employees’ perceptions and experiences of “front stage” areas such as art galleries compared to employees perceptions and experiences of “back stage” areas such as their work spaces? How does it affect the newly transformed museum building’s overall identity, image, spatial layout, and aesthetics?
Vast sums of money spent to design, construct, operate and maintain museum additions demand great accountability of museum leaders and design professionals towards museum visitors and employees. In an age where “starchitects” design buildings from squiggles drawn on cocktail napkins, an urgent need for evidence-based design exists. Evidence from in-depth studies of human factors in relation to design are necessary to respond to visitors’ needs and the experience of viewing art. The museum narrative is framed not only by art objects but also by the space that contains them and how occupants experience this space. More post-occupancy evaluations of high-profile museum additions will help museum leaders and architects understand their successes, shortcomings, and how their designs affect both the visitors and the employees who use them every day.
This study focuses on post-1970 building additions of four premier art museum institutions of the US: the Nelson-Atkins Museum of Art in Kansas City, MO, the Phoenix Art Museum in Phoenix, AZ, the Metropolitan Museum of Art in New York City, NY, and the Art Institute of Chicago in Chicago, IL. It employs a cross-section of methods consisting of assigning space syntactic typologies to museum spaces combined with on-site physical observations in all the four museums mentioned above, a qualitative content analysis of critics’ reviews on additions to all four museums in the popular press—before and after they were built, physical measurements of illuminance of back spaces of the Nelson-Atkins Museum of Art and the Phoenix Art Museum and front spaces of all four museums, and collecting museum employee feedback via an online survey and on-site interviews at the Nelson-Atkins Museum of Art and the Phoenix Art Museum.
Most employees had positive overall opinions of the museum addition and also perceived their fellow employees’ opinions and visitors’ opinions as being positive, but they identified the need to make a number of improvements for accessibility and wayfinding in the museum. Observations confirmed these responses; the front stage spaces of museums for visitors were beset with problems of accessibility and wayfinding in both the new and old parts of the buildings—factors which also affected visitation levels in art galleries. Besides blockbuster shows and special exhibitions, the locations of art galleries (syntactic typologies) in the Met and the Art Institute were found to have an influence on their visitation levels. The lack of adequate amenities such as restrooms, water fountains, and seating, were also found to contribute to museum fatigue in visitors and employees. Museum fatigue had also increased in proportion with building size due to new additions; this was clearly a growing concern among museum employees.
The majority of light levels in art galleries were at optimum settings for art conservation. Many of them, however, did not meet accessibility requirements for ambient lighting, reading text panels, directional signage, and looking at specimens or objects, creating safety concerns and denying equal opportunities to individuals with disabilities. Art gallery lighting also added to the numerous accessibility concerns related to gallery walks, ramps, and wayfinding in all case studies. It was clear that occupants did not share equal status with the art in the museum.
Employee feedback and observations of their work spaces provided insights into the inner workings of art institutions. Results showed that in the process of creating additions, decision-makers mostly ignored the human aspect. New additions with daylighting and other major upgrades in visitor spaces at the Nelson-Atkins Museum and the Phoenix Art Museum did not improve working conditions for employees in back spaces. They worked in spaces that were mostly windowless, without daylight and views, and very often located in basements—in the new museum wings as well as in the older buildings.
This dissertation gives an insider's perspective on the state of the occupants and how and why various decisions were made in museum addition designs. It moves the spotlight away from the usual debates on architectural forms and blockbuster exhibtions, and focuses it on museum occupants instead. By touching on key issues affecting perceptions and experiences of museum employees and visitors, this study bridges the gap between occupants and architectural design while illuminating the myriad ways in which museum additions have been conceived to date. The findings inform stakeholders in museums about the short-term and long-term impact of new additions and provide them with data for making an educated assessment of new museum addition proposals and projects in the future.
Rather than attempting to be a how-to guide on museum additions, this study offers decision-makers a new approach through its findings. In its conclusions, it also offers some recommendations for future museum expansion projects. These recommendations include investing in employee work environments, conducting more internal post-occupancy studies of non-public spaces in the museum, and giving serious consideration to the effects of museum fatigue that arise from the lack of public amenities, wayfinding, and accessibility issues. Inadequate amenities such as water fountains and seating, toilets that are hard to find, and signs that are hard to read or understand can be just as upsetting for the visitor, as a gallery with a famous work of art that is temporarily closed. Museums must work harder to provide these facilities for visitors to be more comfortable and satisfied during their visit. Daylighting in art galleries also plays a significant role in the occupant experience; the key to managing daylighting strategies in museums is finding the right balance between conservation, visual comfort, accessibility, and desired ambience. Museum administrators and architects must identify all these goals from the very beginning when planning new building additions.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2016-03-02 without embargo termsThe student, Altaf Engineer, accepted the attached license on 2015-09-04 at 08:16.The student, Altaf Engineer, submitted this Dissertation for approval on 2015-09-04 at 08:40.This Dissertation was approved for publication on 2015-09-11 at 15:59.DSpace SAF Submission Ingestion Package generated from Vireo submission #8682 on 2016-03-02 at 12:48:57Made available in DSpace on 2016-03-02T19:33:03Z (GMT). No. of bitstreams: 2
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Previous issue date: 2015-09-1
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