Development and validation of a real-time quantitative PCR assay for the detection and quantification of Perkinsus marinus in the Eastern oyster, Crassostrea virginica

Author Posting. © National Shellfisheries Association, 2009. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 28 (2009): 459-464, doi:10.2983/035.028.0306.Perkinus marinus causes a devastating disease, known as Dermo, in the Eastern oyster Crassostrea virginica. Routine detection of the disease is traditionally accomplished by the use of the Ray/Makin assay, using Fluid Thioglycollate Medium (RFTM). A simple real-time quantitative PCR assay was developed as a diagnostic tool to detect and quantify P. marinus, to complement and serve as an alternate to the RFTM method. Using a dual-labeled probe approach, a sensitive assay was designed to accurately detect a range of one to several thousand P. marinus organisms present in oyster tissues. A simple extraction method was used to increase throughput of the assay. Cultured P. marinus cells were quantified prior to DNA extraction, generating a standard curve and allowing cell counts to be derived from PCR cycle threshold values. Direct comparison of the RFTM and real-time PCR methods was accomplished by using tissue samples from the same oyster for both tests. Plotting cycle threshold values against the known Mackin index value generated a standard curve with a coefficient of regression of 0.9. Our results indicate that correlations could be made between this molecular based approach and traditional methods, allowing results generated from the PCR assay to be easily translated into the understood Mackin scale

A Longitudinal Study of Engineering Student Performance and Retention. V. Comparisons with Traditionally-Taught Students

In a longitudinal study at North Carolina State University, a cohort of students took five chemical engineering courses taught by the same instructor in five consecutive semesters. The courses made extensive use of active and cooperative learning and a variety of other techniques designed to address a broad spectrum of learning styles. Previous reports on the study summarized the instructional methods used in the experimental course sequence, described the performance of the cohort in the introductory chemical engineering course, and examined performance and attitude differences between students from rural and urban backgrounds and between male and female students.1–4 This paper compares outcomes for the experimental cohort with outcomes for students in a traditionally‐taught comparison group. The experimental group outperformed the comparison group on a number of measures, including retention and graduation in chemical engineering, and many more of the graduates in this group chose to pursue advanced study in the field. Since the experimental instructional model did not require small classes (the smallest of the experimental classes had 90 students) or specially equipped classrooms, it should be adaptable to any engineering curriculum at any institution

The Effects of Personality Type on Engineering Student Performance and Attitudes

The Myers‐Briggs Type Indicator® (MBTI) was administered to a group of 116 students taking the introductory chemical engineering course at North Carolina State University. That course and four subsequent chemical engineering courses were taught in a manner that emphasized active and cooperative learning and inductive presentation of course material. Type differences in various academic performance measures and attitudes were noted as the students progressed through the curriculum. The observations were generally consistent with the predictions of type theory, and the experimental instructional approach appeared to improve the performance of MBTI types (extraverts, sensors, and feelers) found in previous studies to be disadvantaged in the engineering curriculum. The conclusion is that the MBTI is a useful tool for helping engineering instructors and advisors to understand their students and to design instruction that can benefit all of them

UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

A Methodology to directly input data from an uncontrolled aerial photograph into a vector based geographic information system

Historically the U.S. Forest Service has used uncorrected aerial photographs to delineate proposed and past management activities on the land base it manages. Transferring a boundary from an image not planimetrically correct to a planimetrically corrected image introduces errors. Positional accuracy of boundaries affects the number of acres the Forest is accountable for managing, and the annual sale quantity (ASQ) or annual board feet targets. The purpose of this study was to develop a methodology that eliminated the need to transfer the boundary from an uncorrected to a corrected image. Raster and vector warping methods were evaluated with reference to positional accuracy and efficiency. Due to the rugged topography of the Siuslaw National Forest, selection of ground control points (GCPs) was an important function in the accurate transformation of images. A Vector warping method, Rubber Sheeting the ARC/INFO projective transformation for all digital GCPs, to all of the Global Position System (GPS) ground control points, provided the most accurate rectification of vector boundaries that had been digitized or scanned from an uncontrolled low elevation photograph

Efficient Acoustic Feature Computation Using FPGAs

Many recent advances in music information retrieval (MIR) have been data-driven. Widespread performance evaluations on common data sets, like the annual MIREX events, have been instrumental in advancing the field. Such endeavors incur large computational costs and could potentially benefit from faster calculation of acoustic features. Traditional cluster-based solutions are expensive and space- and power inefficient. The massively parallel architecture of the field programmable gate array (FPGA) makes it possible to design lower-cost, applicationspecific chips rivaling cluster speed for large-scale acoustic feature computation. Such devices also show potential for implementations of MIR systems on embedded devices where hardware acceleration is a necessity. We present a prototype Xilinx System Generator (XSG) library for acoustic feature calculation. We use a genre classification task to compare the performance of simulated hardware features to those computed using standard methods. Finally, we discuss ongoing efforts toward a working hardware design

Preparing medical students to recognize and respond to gender based violence in Nigeria

Background: Medical practitioners are ideally positioned to mitigate the impact of gender based violence (GBV) on the health of victims.  However, there is a lack of information on students’ ability and willingness to do so. Objective:  To identify factors which impact on students’ attainment of the knowledge and perceived ability to manage victims. Methods: A cross-sectional survey was conducted on 388 (91.5%) final year medical students from three medical schools in South West, Nigeria.   Results: Students were knowledgeable on sexual (63.7%) and physical (54.6%) forms of GBV and unfamiliar with other forms. The mean scores for knowledge (7.1 ± 2.5 out of 11); attitude (52.6 ± 10.3 out of 80); personal comfort (44.1 ± 10.0 out of 65) and skills (3.1 ± 2.6 out of 7) were calculated.  Younger respondents, females and married students reported less skill to manage victims.  The location of school, previous training and personal comfort remained significant determinants of students’ self reported skills on GBV. Respondents with prior training on GBV and comfortable with managing patients, were four times more likely to perceive they were more skilled than their peers [AOR = 4.33, 95% CI: 2.37 – 7.90 and AOR 3.53; 95% CI 2.16- 5.78 respectively]. Conclusion: Formalised skills training on GBV is a necessity, especially for young, female students and training cannot be left to serendipity. The medical curriculum should be reviewed.Keywords: Undergraduate medical curriculum, gender based violence, violence against women, medical student perceptions, teaching and training undergraduate

UPC++: A high-performance communication framework for asynchronous computation

UPC++ is a C++ library that supports high-performance computation via an asynchronous communication framework. This paper describes a new incarnation that differs substantially from its predecessor, and we discuss the reasons for our design decisions. We present new design features, including future-based asynchrony management, distributed objects, and generalized Remote Procedure Call (RPC). We show microbenchmark performance results demonstrating that one-sided Remote Memory Access (RMA) in UPC++ is competitive with MPI-3 RMA; on a Cray XC40 UPC++ delivers up to a 25% improvement in the latency of blocking RMA put, and up to a 33% bandwidth improvement in an RMA throughput test. We showcase the benefits of UPC++ with irregular applications through a pair of application motifs, a distributed hash table and a sparse solver component. Our distributed hash table in UPC++ delivers near-linear weak scaling up to 34816 cores of a Cray XC40. Our UPC++ implementation of the sparse solver component shows robust strong scaling up to 2048 cores, where it outperforms variants communicating using MPI by up to 3.1x. UPC++ encourages the use of aggressive asynchrony in low-overhead RMA and RPC, improving programmer productivity and delivering high performance in irregular applications

UPC++ v1.0 Programmer’s Guide, Revision 2019.9.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

UPC++ v1.0 Specification, Revision 2019.9.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied