A novel method for rapid and selective extraction of male DNA from rape kits using alkaline lysis and pressure cycling technology (PCT)

There is an increasing demand for DNA analysis because of the sensitivity of the method and the ability to uniquely identify and distinguish individuals with a high degree of certainty. But this demand has led to huge backlogs in evidence lockers since the current DNA extraction protocols require long processing time. The DNA analysis procedure becomes more complicated when analyzing sexual assault casework samples where the evidence contains more than one contributor. Additional processing to separate different cell types in order to simplify the final data interpretation further contributes to the existing cumbersome protocols. The goal of the present project is to develop a rapid and efficient extraction method that permits selective digestion of mixtures. ^ Selective recovery of male DNA was achieved with as little as 15 minutes lysis time upon exposure to high pressure under alkaline conditions. Pressure cycling technology (PCT) is carried out in a barocycler that has a small footprint and is semi-automated. Typically less than 10% male DNA is recovered using the standard extraction protocol for rape kits, almost seven times more male DNA was recovered from swabs using this novel method. Various parameters including instrument setting and buffer composition were optimized to achieve selective recovery of sperm DNA. Some developmental validation studies were also done to determine the efficiency of this method in processing samples exposed to various conditions that can affect the quality of the extraction and the final DNA profile. ^ Easy to use interface, minimal manual interference and the ability to achieve high yields with simple reagents in a relatively short time make this an ideal method for potential application in analyzing sexual assault samples.^

Sea surface and the sea floor regionalization of the Southern Ocean by multivariate cluster analysis, links to ArcGIS project files

This study subdivides the Weddell Sea, Antarctica, into seafloor regions using multivariate statistical methods. These regions are categories used for comparing, contrasting and quantifying biogeochemical processes and biodiversity between ocean regions geographically but also regions under development within the scope of global change. The division obtained is characterized by the dominating components and interpreted in terms of ruling environmental conditions. The analysis uses 28 environmental variables for the sea surface, 25 variables for the seabed and 9 variables for the analysis between surface and bottom variables. The data were taken during the years 1983-2013. Some data were interpolated. The statistical errors of several interpolation methods (e.g. IDW, Indicator, Ordinary and Co-Kriging) with changing settings have been compared for the identification of the most reasonable method. The multivariate mathematical procedures used are regionalized classification via k means cluster analysis, canonical-correlation analysis and multidimensional scaling. Canonical-correlation analysis identifies the influencing factors in the different parts of the cove. Several methods for the identification of the optimum number of clusters have been tested. For the seabed 8 and 12 clusters were identified as reasonable numbers for clustering the Weddell Sea. For the sea surface the numbers 8 and 13 and for the top/bottom analysis 8 and 3 were identified, respectively. Additionally, the results of 20 clusters are presented for the three alternatives offering the first small scale environmental regionalization of the Weddell Sea. Especially the results of 12 clusters identify marine-influenced regions which can be clearly separated from those determined by the geological catchment area and the ones dominated by river discharge.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.

Development of an Efficient Genome Editing Method by CRISPR/Cas9 in a Fish Cell Line

This project was carried out during CD’s BBSRC Eastbio PIPS placement at Marine Scotland. The authors are grateful to Dr Milena Monte (University of Aberdeen) for help with the FACS analysis. The authors wish to thank Dr Filippo Del Bene (Neuronal Circuit Development, Institut Curie) and Dr Wenbiao Chen (School of Medicine, Vanderbilt University) for the Addgene plasmids, #61051 and #47929, respectively, and Prof. Nancy C. Reich Marshall (Department of Molecular Genetics and Microbiology, Stony Brooks University) for the plasmid pmEGFP-N1.

A Novel Method for Rapid and Selective Extraction of Male DNA from Rape Kits using Alkaline Lysis and Pressure Cycling Technology (PCT)

There is an increasing demand for DNA analysis because of the sensitivity of the method and the ability to uniquely identify and distinguish individuals with a high degree of certainty. But this demand has led to huge backlogs in evidence lockers since the current DNA extraction protocols require long processing time. The DNA analysis procedure becomes more complicated when analyzing sexual assault casework samples where the evidence contains more than one contributor. Additional processing to separate different cell types in order to simplify the final data interpretation further contributes to the existing cumbersome protocols. The goal of the present project is to develop a rapid and efficient extraction method that permits selective digestion of mixtures. Selective recovery of male DNA was achieved with as little as 15 minutes lysis time upon exposure to high pressure under alkaline conditions. Pressure cycling technology (PCT) is carried out in a barocycler that has a small footprint and is semi-automated. Typically less than 10% male DNA is recovered using the standard extraction protocol for rape kits, almost seven times more male DNA was recovered from swabs using this novel method. Various parameters including instrument setting and buffer composition were optimized to achieve selective recovery of sperm DNA. Some developmental validation studies were also done to determine the efficiency of this method in processing samples exposed to various conditions that can affect the quality of the extraction and the final DNA profile. Easy to use interface, minimal manual interference and the ability to achieve high yields with simple reagents in a relatively short time make this an ideal method for potential application in analyzing sexual assault samples.

Modeling of a Heat-Induced Buckling of Plates Using the Mesh-free Method

In the process of engineering design of structural shapes, the flat plate analysis results can be generalized to predict behaviors of complete structural shapes. In this case, the purpose of this project is to analyze a thin flat plate under conductive heat transfer and to simulate the temperature distribution, thermal stresses, total displacements, and buckling deformations. The current approach in these cases has been using the Finite Element Method (FEM), whose basis is the construction of a conforming mesh. In contrast, this project uses the mesh-free Scan Solve Method. This method eliminates the meshing limitation using a non-conforming mesh. I implemented this modeling process developing numerical algorithms and software tools to model thermally induced buckling. In addition, convergence analysis was achieved, and the results were compared with FEM. In conclusion, the results demonstrate that the method gives similar solutions to FEM in quality, but it is computationally less time consuming.

Integrated Construction Project Delivery System in the U.S. Public Sector: An Information Modeling Framework

Integrated project delivery (IPD) method has recently emerged as an alternative to traditional delivery methods. It has the potential to overcome inefficiencies of traditional delivery methods by enhancing collaboration among project participants. Information and communication technology (ICT) facilitates IPD by effective management, processing and communication of information within and among organizations. While the benefits of IPD, and the role of ICT in realizing them, have been generally acknowledged, the US public construction sector is very slow in adopting IPD. The reasons are - lack of experience and inadequate understanding of IPD in public owner as confirmed by the results of the questionnaire survey conducted under this research study. The public construction sector should be aware of the value of IPD and should know the essentials for effective implementation of IPD principles - especially, they should be cognizant of the opportunities offered by advancements in ICT to realize this. In order to address the need an IPD Readiness Assessment Model (IPD-RAM) was developed in this research study. The model was designed with a goal to determine IPD readiness of a public owner organization considering selected IPD principles, and ICT levels, at which project functions were carried out. Subsequent analysis led to identification of possible improvements in ICTs that have the potential to increase IPD readiness scores. Termed as the gap identification, this process was used to formulate improvement strategies. The model had been applied to six Florida International University (FIU) construction projects (case studies). The results showed that the IPD readiness of the organization was considerably low and several project functions can be improved by using higher and/or advanced level ICT tools and methods. Feedbacks from a focus group comprised of FIU officials and an independent group of experts had been received at various stages of this research and had been utilized during development and implementation of the model. Focus group input was also helpful for validation of the model and its results. It was hoped that the model developed would be useful to construction owner organizations in order to assess their IPD readiness and to identify appropriate ICT improvement strategies.

The Antibiotic Resistance and Prescribing in European Children Project: A Neonatal and Pediatric Antimicrobial Web-based Point Prevalence Survey in 73 Hospitals Worldwide

BACKGROUND: The neonatal and pediatric antimicrobial point prevalence survey (PPS) of the Antibiotic Resistance and Prescribing in European Children project (http://www.arpecproject.eu/) aims to standardize a method for surveillance of antimicrobial use in children and neonates admitted to the hospital within Europe. This article describes the audit criteria used and reports overall country-specific proportions of antimicrobial use. An analytical review presents methodologies on antimicrobial use.

METHODS: A 1-day PPS on antimicrobial use in hospitalized children was organized in September 2011, using a previously validated and standardized method. The survey included all inpatient pediatric and neonatal beds and identified all children receiving an antimicrobial treatment on the day of survey. Mandatory data were age, gender, (birth) weight, underlying diagnosis, antimicrobial agent, dose and indication for treatment. Data were entered through a web-based system for data-entry and reporting, based on the WebPPS program developed for the European Surveillance of Antimicrobial Consumption project.

RESULTS: There were 2760 and 1565 pediatric versus 1154 and 589 neonatal inpatients reported among 50 European (n = 14 countries) and 23 non-European hospitals (n = 9 countries), respectively. Overall, antibiotic pediatric and neonatal use was significantly higher in non-European (43.8%; 95% confidence interval [CI]: 41.3-46.3% and 39.4%; 95% CI: 35.5-43.4%) compared with that in European hospitals (35.4; 95% CI: 33.6-37.2% and 21.8%; 95% CI: 19.4-24.2%). Proportions of antibiotic use were highest in hematology/oncology wards (61.3%; 95% CI: 56.2-66.4%) and pediatric intensive care units (55.8%; 95% CI: 50.3-61.3%).

CONCLUSIONS: An Antibiotic Resistance and Prescribing in European Children standardized web-based method for a 1-day PPS was successfully developed and conducted in 73 hospitals worldwide. It offers a simple, feasible and sustainable way of data collection that can be used globally.

Analyzing Gene Centres with the Help of the Checklist Method – the Case of Syria

The present survey of species diversity of cultivated plants is the first for Syria. Some cultivated species will be added in the future, because due to the civil war in Syria, it was not possible to visit the country in the frame of the present work, as initially planned. Checklists proved to be a useful tool for overviewing the cultivated plants of selected areas and allow a characterization of the state of plant genetic resources of Syria. Syria has experienced several civilizations. Man settled in this productive land since ancient times and used its resources. However, such use has led to changes in vegetation and decline of wildlife through the country, in seashore areas, interior, mountains, and grassland. Plant domestication and growing started more than 10,000 years ago in West Asia. Since then, plentiful of economic plant species were present and used by man and his domesticated animals. Forming a part of the Fertile Crescent, where many of the world’s agricultural plants have evolved, Syria is extremely rich in agrobiodiversity. Wild progenitors of wheat and barley and wild relatives of many fruit trees such as almonds and pistachio as well as forage species are still found in marginal lands and less disturbed areas. These are threatened by a wide range of human activities, notably modern, extensive agriculture, overgrazing, overcutting and urban expansion. Syria is also considered as part of one of the main centres of origin, according to Vavilov, who had collected in Syria in 1926. The first expeditions to crop fields showed the exclusive nature of cultivated plants in Syria with a high number of endemic forms. Furthermore, Syria is a part of a biodiversity hotspot. Several studies have been performed to study agrobiodiversity in different parts of Syria, but usually on wild species. Many collections have been carried out; however, they focussed preferably on cereals and pulses, and particularly on wheat, like Vavilov’s expedition. Only 30 crops make up the major part of the conserved Syrian crop plant material in the genebank, indicating that most of the remaining 7,000 species of cultivated plants and many other valuable genetic resources species have only been included on a limited scale in the genebank collections. Although a small country (185,180 km2), Syria accommodates numerous ecosystems that allow for a large diversity of plant genetic resources for agriculture ranging from cold-requiring to subtropical crops to live and thrive. Only few references are available in this respect. The aim of the present study was to complete a checklist of Syria’s cultivated plants of agriculture and horticulture excluding plants only grown as ornamental or for forestry. Furthermore, plants taken for reforestation have not been included, if they do not have also agricultural or horticultural uses. Therefore, the inclusion of plants into the checklist follows the same principles as “Mansfeld’s Encyclopedia”. Main sources of information were published literature, floras of Syria, Lebanon and the Mediterranean, as well as Syrian printed sources in Arabic and/or English, reports from FAO on agricultural statistics in Syria, and data from ICARDA and Bioversity International. In addition, personal observations gathered during professional work in the General Commission for Scientific Agricultural Research (GCSAR) in Syria (since 1989) and participation in projects were taken into account. These were: (1) A project on “Conservation and Sustainable Use of Dry Land Agrobiodiversity in the Near East” with participation of Jordan, Lebanon, Syria, and the Palestinian Authority, focussing on landraces and wild relatives of barley, wheat, lentil, alliums, feed legumes, and fruit trees (1999–2005). (2) A project for vegetable landraces (1993–1995) in collaboration with the former International Plant Genetic Resources Institute and the UN Development Programme, in which 380 local vegetable accessions were evaluated. For medicinal plants and fruit trees I was in personal contact with departments of GCSAR and the Ministry of Agriculture and Agrarian Reform, as well as with private organizations. The resulting checklist was compared with the catalogues of crop plants of Italy and a checklist of cultivated plants of Iraq. The cultivated plant species are presented in alphabetical order according to their accepted scientific names. Each entry consists of a nomenclatural part, folk names, details of plant uses, the distribution in Syria (by provinces), a textual description, and references to literature. In total, 262 species belonging to 146 genera and 57 families were identified. Within-species (intraspecific) diversity is a significant measure of the biodiversity. Intraspecific diversity for wild plants has been and remains to be well studied, but for crop plants there are only few results. Mansfeld’s method is an actual logical contribution to such studies. Among the families, the following have the highest number of crop species: Leguminosae (34 spp.), Rosaceae (24), Gramineae (18), Labiatae (18), Compositae (14), Cruciferae (14), Cucurbitaceae (11), Rutaceae (10), Malvaceae (9), Alliaceae (7), and Anacardiaceae (7). The establishment of an effective programme for the maintenance of plant genetic resources in Syria started in the mid-1970s. This programme considered ex situ and in situ collection of the genetic resources of various field crops, fruit trees and vegetables. From a plant genetic resources viewpoint, it is clear that the homegarden is an important location for the cultivation of so-called neglected and underutilized species (neglected from a research side and underutilized from a larger economic side). Such species have so far not received much care from ecologists, botanists and agronomists, and they are considerably under-represented in genebanks.

Development of a Rational Characterization Method for Iowa Fly Ash, HR-286, Annual Progress Report 1, 1986

The following report summarizes research activities on the project for the period December 1, 1985 through November 31, 1986. Research efforts for the first year have proceeded basically as outlined in the project proposal.

Development of a Rational Characterization Method for Iowa Fly Ash, HR-286, Annual Progress Report 2, 1987

The following report summarizes research activities on the project for the period December 1, 1986 to November 30, 1987. Research efforts for the second year deviated slightly from those described in the project proposal. By the end of the second year of testing, it was possible to begin evaluating how power plant operating conditions influenced the chemical and physical properties of fly ash obtained from one of the monitored power plants (Ottumwa Generating Station, OGS). Hence, several of the tasks initially assigned to the third year of the project (specifically tasks D, E, and F) were initiated during the second year of the project. Manpower constraints were balanced by delaying full scale implementation of the quantitative X-ray diffraction and differential thermal analysis tasks until the beginning of the third year of the project. Such changes should have little bearing on the outcome of the overall project.

Highway Location Reference Procedure Project, 1990

The purpose of the proposed Highway Location Reference Procedure is stated in the contract as follows: "Establishment of a highway network locational reference process that will primarily allow for the proper correlation of pavement management data, and secondarily provide the basis for other existing and future data base integration and for the planned Iowa DOT Geographic Information System. In addition, the locational reference process will be able to correlate network applications with a statewide spatial location method to facilitate the relationship of Iowa DOT data to that of other agencies and to allow for the graphic display of the network in map form." The Design Specifications and Implementation Plan, included in this Final Report, are intended to provide the basis for proceeding with immediate development and implementation of the pavement management system. These specifications will also support the future Iowa DOT implementation of other integrated data bases and/or the planned Geographic Information System.

Understanding the Patient Experience Through the Power of Film: a Mixed Method Qualitative Research Study

Background For decades film has proved to be a powerful form of communication. Whether produced as entertainment, art or documentary, films have the capacity to inform and move us. Films are a highly attractive teaching instrument and an appropriate teaching method in health education. It is a valuable tool for studying situations most transcendental to human beings such as pain, disease and death. Objectives The objectives were to determine how this helps students engage with their role as health care professionals; to determine how they view the personal experience of illness, disease, disability or death; and to determine how this may impact upon their provision of patient care. Design, Setting and Participants The project was underpinned by the film selection determined by considerate review, intensive scrutiny, contemplation and discourse by the research team. 7 films were selected, ranging from animation; foreign, documentary, biopic and Hollywood drama. Each film was shown discretely, in an acoustic lecture theatre projected onto a large screen to pre-registration student nurses (adult, child and mental health) across each year of study from different cohorts (n = 49). Method A mixed qualitative method approach consisted of audio-recorded 5-minute reactions post film screening; coded questionnaires; and focus group. Findings were drawn from the impact of the films through thematic analysis of data sets and subjective text condensation categorised as: new insights looking through patient eyes; evoking emotion in student nurses; spiritual care; going to the moves to learn about the patient experience; self discovery through films; using films to link theory to practice. Results Deeper learning through film as a powerful medium was identified in meeting the objectives of the study. Integration of film into pre registration curriculum, pedagogy, teaching and learning is recommended. Conclusion The teaching potential of film stems from the visual process linked to human emotion and experience. Its impact has the power to not only help in learning the values that underpin nursing, but also for respecting the patient experience of disease, disability, death and its reality.

Drawing in Duos: The Journeys and Intersections Collaboration Project Between Istanbul and Worcester

This paper focuses on a collaborative drawing project carried out between two undergraduate drawing courses, one in İstanbul and the other in Worcester, during the Fall 2015 semester. Duos -teams of two working remotely- took turns to work on the same drawing in correspondence for three months by means of communication and sharing the changing images on-line with one another. The project introduced a collaborative method of learning based on drawing, initiated cultural exchange and cooperation. The role of drawing in the project was critical due to the direct but gradual nature of transmitting meaning onto paper. Outcomes of this project consisted of a flexible and playful creation process for students making use of the element of chance. They sought alternate ways to finalize a drawing and experienced the benefits of artistic co-production. The project has the capacity to inspire artists, instructors and others interested in creative partnership in different disciplines and can be of value as an educational model.

Defining the Resolution of a Network for Transportation Analyses: a New Method to Improve Transportation Planning Decisions

Travel demand models are important tools used in the analysis of transportation plans, projects, and policies. The modeling results are useful for transportation planners making transportation decisions and for policy makers developing transportation policies. Defining the level of detail (i.e., the number of roads) of the transport network in consistency with the travel demand model’s zone system is crucial to the accuracy of modeling results. However, travel demand modelers have not had tools to determine how much detail is needed in a transport network for a travel demand model. This dissertation seeks to fill this knowledge gap by (1) providing methodology to define an appropriate level of detail for a transport network in a given travel demand model; (2) implementing this methodology in a travel demand model in the Baltimore area; and (3) identifying how this methodology improves the modeling accuracy. All analyses identify the spatial resolution of the transport network has great impacts on the modeling results. For example, when compared to the observed traffic data, a very detailed network underestimates traffic congestion in the Baltimore area, while a network developed by this dissertation provides a more accurate modeling result of the traffic conditions. Through the evaluation of the impacts a new transportation project has on both networks, the differences in their analysis results point out the importance of having an appropriate level of network detail for making improved planning decisions. The results corroborate a suggested guideline concerning the development of a transport network in consistency with the travel demand model’s zone system. To conclude this dissertation, limitations are identified in data sources and methodology, based on which a plan of future studies is laid out.