Learning Upper Level Molecular Biology Using the Yeast Two-Hybrid (Y2h) System

A challenge with upper level biology labs is that experiments cannot normally be done in a 3-hour window. It can also be a challenge to stay motivated when doing labs with predetermined outcomes. Third, a “one size fits all” laboratory can be boring for those of us with previous experience. Finally, having to share a small lab space with many classmates simultaneously makes working efficiently difficult. An unexpectedly large enrollment in our molecular biology lab course provided our professor with an opportunity to use a class project to address the above concerns. One of our professors has a collection of clones from an initial Y2H screen for proteins that interact with a myosin protein. Each of us was assigned 3 clones in yeast that we characterized. This included plasmid isolation from yeast, transformation of E. coli, plasmid isolation from E. coli, DNA quantitation, restriction analysis, DNA sequencing, and BLAST analysis to identify and characterize our clones. We could not begin our research until we had verbally demonstrated understanding of the Y2H system to the instructor. We needed our lab notebook signed before each step in the process, which we could then do at any time the lab was open. Results were presented in a formal lab report. This approach allowed us to take ownership of our projects, troubleshoot problems, and learn techniques on our own. It also staggered the use of lab space and facilities, allowing more of us to work on our own time, while less experienced students could use the regular time block with more instructor availability. This lab was a positive learning experience; we got a better feel for the nature of scientific research, gained independence in the lab and were more invested in obtaining results

Ultra-wideband radar for simultaneous and unobtrusive monitoring of respiratory and heart rates in early childhood:A Deep Transfer Learning Approach

Unobtrusive monitoring of children’s heart rate (HR) and respiratory rate (RR) can be valuable for promoting the early detection of potential health issues, improving communication with healthcare providers and reducing unnecessary hospital visits. A promising solution for wireless vital sign monitoring is radar technology. This paper presents a novel approach for the simultaneous estimation of children’s RR and HR utilizing ultra-wideband (UWB) radar using a deep transfer learning algorithm in a cohort of 55 children. The HR and RR are calculated by processing radar signals via spectrogram from time epochs of 10 s (25 sample length of hamming window with 90% overlap) and then transforming the resultant representation into 2-dimensional images. These images were fed into a pre-trained Visual Geometry Group-16 (VGG-16) model (trained on ImageNet dataset), with weights of five added layers fine-tuned using the proposed data. The prediction on the test data achieved a mean absolute error (MAE) of 7.3 beats per minute (BPM &lt; 6.5% of average HR) and 2.63 breaths per minute (BPM &lt; 7% of average RR). We also achieved a significant Pearson’s correlation of 77% and 81% between true and extracted for HR and RR, respectively. HR and RR samples are extracted every 10 s.</p

CORE Technology and Exact Hamiltonian Real-Space Renormalization Group Transformations

The COntractor REnormalization group (CORE) method, a new approach to solving Hamiltonian lattice systems, is presented. The method defines a systematic and nonperturbative means of implementing Kadanoff-Wilson real-space renormalization group transformations using cluster expansion and contraction techniques. We illustrate the approach and demonstrate its effectiveness using scalar field theory, the Heisenberg antiferromagnetic chain, and the anisotropic Ising chain. Future applications to the Hubbard and t-J models and lattice gauge theory are discussed.Comment: 65 pages, 9 Postscript figures, uses epsf.st

Symplectically degenerate maxima via generating functions

We provide a simple proof of a theorem due to Nancy Hingston, asserting that symplectically degenerate maxima of any Hamiltonian diffeomorphism of the standard symplectic 2d-torus are non-isolated contractible periodic points or their action is a non-isolated point of the average-action spectrum. Our argument is based on generating functions.Comment: 25 pages, thoroughly revised version, new titl

Molecular Characterization of Haemaphysalis Species and a Molecular Genetic Key for the Identification of Haemaphysalis of North America

Haemaphysalis longicornis (Acari: Ixodidae), the Asian longhorned tick, is native to East Asia, but has become established in Australia and New Zealand, and more recently in the United States. In North America, there are other native Haemaphysalis species that share similar morphological characteristics and can be difficult to identify if the specimen is damaged. The goal of this study was to develop a cost-effective and rapid molecular diagnostic assay to differentiate between exotic and native Haemaphysalis species to aid in ongoing surveillance of H. longicornis within the United States and help prevent misidentification. We demonstrated that restriction fragment length polymorphisms (RFLPs) targeting the 16S ribosomal RNA and the cytochrome c oxidase subunit I (COI) can be used to differentiate H. longicornis from the other Haemaphysalis species found in North America. Furthermore, we show that this RFLP assay can be applied to Haemaphysalis species endemic to other regions of the world for the rapid identification of damaged specimens. The work presented in this study can serve as the foundation for region specific PCR-RFLP keys for Haemaphysalis and other tick species and can be further applied to other morphometrically challenging taxa

The Maslov index in weak symplectic functional analysis

We recall the Chernoff-Marsden definition of weak symplectic structure and give a rigorous treatment of the functional analysis and geometry of weak symplectic Banach spaces. We define the Maslov index of a continuous path of Fredholm pairs of Lagrangian subspaces in continuously varying Banach spaces. We derive basic properties of this Maslov index and emphasize the new features appearing.Comment: 34 pages, 13 figures, 45 references, to appear in Ann Glob Anal Geom. The final publication will be available at http://www.springerlink.com. arXiv admin note: substantial text overlap with arXiv:math/040613

Two-Component Direct Fluorescent-Antibody Assay for Rapid Identification of Bacillus anthracis

A two-component direct fluorescent-antibody (DFA) assay, using fluorescein-labeled monoclonal antibodies specific to the Bacillus anthracis cell wall (CW-DFA) and capsule (CAP-DFA) antigens, was evaluated and validated for rapid identification of B. anthracis. We analyzed 230 B. anthracis isolates; 228 and 229 were positive by CW-DFA and CAP-DFA assays, respectively. We also tested 56 non–B. anthracis strains; 10 B. cereus and 2 B. thuringiensis were positive by the CW-DFA assay, and 1 B. megaterium strain was positive by CAP-DFA. Analysis of the combined DFA results identified 227 of 230 B. anthracis isolates; all 56 strains of the other Bacillus spp. were negative. Both DFA assays tested positive on 14 of 26 clinical specimens from the 2001 anthrax outbreak investigation. The two-component DFA assay is a sensitive, specific, and rapid confirmatory test for B. anthracis in cultures and may be useful directly on clinical specimens

A K-theoretical Invariant and Bifurcation for Homoclinics of Hamiltonian Systems

We revisit a K-theoretical invariant that was invented by the first author some years ago for studying multiparameter bifurcation of branches of critical points of functionals. Our main aim is to apply this invariant to investigate bifurcation of homoclinic solutions of families of Hamiltonian systems which are parametrised by tori

Pseudotumoural soft tissue lesions of the foot and ankle: a pictorial review

In the foot and ankle region, benign neoplasms and pseudotumoural soft tissue lesions are significantly more frequent than malignant tumours. The pseudotumoural lesions constitute a heterogeneous group, with highly varied aetiology and histopathology. This article reviews the imaging features of the most common pseudotumours of the soft tissues in the foot and ankle. Although the imaging characteristics of several of the lesions discussed are non-specific, combining them with lesion location and clinical features allows the radiologist to suggest a specific diagnosis in most cases