A Comparison of Step-Detection Methods: How Well Can You Do?

Many biological machines function in discrete steps, and detection of such steps can provide insight into the machines’ dynamics. It is therefore crucial to develop an automated method to detect steps, and determine how its success is impaired by the significant noise usually present. A number of step detection methods have been used in previous studies, but their robustness and relative success rate have not been evaluated. Here, we compare the performance of four step detection methods on artificial benchmark data (simulating different data acquisition and stepping rates, as well as varying amounts of Gaussian noise). For each of the methods we investigate how to optimize performance both via parameter selection and via prefiltering of the data. While our analysis reveals that many of the tested methods have similar performance when optimized, we find that the method based on a chi-squared optimization procedure is simplest to optimize, and has excellent temporal resolution. Finally, we apply these step detection methods to the question of observed step sizes for cargoes moved by multiple kinesin motors in vitro. We conclude there is strong evidence for sub-8-nm steps of the cargo’s center of mass in our multiple motor records.     

Confocal Laser Scanning Microscopy Evaluation of an Acellular Dermis Tissue Transplant (Epiflex?)

The structure of a biological scaffold is a major determinant of its biological characteristics and its interaction with cells. An acellular dermis tissue transplant must undergo a series of processing steps, to remove cells and genetic material and provide the sterility required for surgical use. During manufacturing and sterilization the structure and composition of tissue transplants may change.The composition of the human cell-free dermis transplant Epiflex® was investigated with specific attention paid to its structure, matrix composition, cellular content and biomechanics.We demonstrated that after processing, the structure of Epiflex remains almost unchanged with an intact collagen network and extracellular matrix (ECM) protein composition providing natural cell interactions. Although the ready to use transplant does contain some cellular and DNA debris, the processing procedure results in a total destruction of cells and active DNA which is a requirement for an immunologically inert and biologically safe substrate. Its biomechanical parameters do not change significantly during the processing.     

It’s Our Fault: A Global Comparison of Different Ways of Explaining Climate Change

Human Ecology - International surveys suggest people increasingly agree the climate is changing and humans are the cause. One reading of this is that people have adopted the scientific point of...     

Chest Contour—A Comparison of American and Russian Track Stars

Measurement of the chests and other physical features of United States and Soviet Russian track and field stars showed the Americans broader chested, taller, lighter in weight and about two and a half years younger.Comparison of the measurements of the American group with those made on the 1940 and 1949 N.C.A.A. track and field stars in a previous study indicated that the Americans are developing relatively broader, flatter chests and are growing taller.     

Confocal Laser Endomicroscopy for In Vivo Diagnosis of Clostridium difficile Associated Colitis — A Pilot Study

Background

Clostridium difficile infection (CDI) is one of the most dreaded causes of hospital-acquired diarrhea. Main objective was to investigate whether confocal laser endomicroscopy (CLE) has the capability for in vivo diagnosis of C. difficile associated histological changes. Second objective was to prove the presence of intramucosal bacteria using CLE.

Methods

80 patients were prospectively included, 10 patients were diagnosed with CDI based on toxigenic culture. To validate the presence of intramucosal bacteria ex vivo, CLE was performed in pure C. difficile culture; additionally fluorescence in situ hybridization (FISH) was performed. Finally, CLE with fluorescence labelled oligonucleotide probe specific for C. difficile was performed ex vivo in order to prove the presence of bacteria.

Results

CLE identified CDI-associated histological changes in vivo (sensitivity and accuracy of 88.9% and 96.3%). In addition, intramucosal bacteria were visualized. The presence of these bacteria could be proven by CLE with labeled, specific molecular C. difficile probe and FISH-technique. Based on comparison between CLE and FISH analyses, sensitivity and specificity for the presence of intramucosal bacteria were 100%.

Conclusion

CLE has the potential for in vivo diagnosis of CDI associated colitis. In addition, CLE allowed the detection of intramucosal bacteria in vivo.     

ADENOTONSILLECTOMY—Indications and Application of Surgical Techniques

As a result of audiometric surveys in public schools, many children are being referred to physicians for further examination and definitive treatment. Therefore, the indications for adenotonsillectomy are reviewed.It is believed that the operation should not be done in infants with congenital deafness until full study of the problem has been completed, and that it should not be done routinely in children in whom there is no positive indication for it. When the operation is done, as much normal mucosa as possible should be saved. Closing the superior aspect of the incision with chromic suture is recommended as a means of avoiding a vertical band of scar tissue which may divide the tonsillar fossa into two parts.     

Is an Idea Different from Cake: Can You Have It and Eat It,Too? A Violation of Permanence in Information Consumption

One of the basic features of information is permanence. This feature states that the consumption of information by one consumer does not affect the availability of that information to other consumers. We present examples in two studies indicating that both laymen and experts of information exchange may be motivated to make choices that violate the permanence feature in accepting (Study 1) and offering (Study 2) information. When they possess, but have not yet consumed information, people may suffer from the appearance of wastefulness. This apparent wastefulness may provide a potential explanation for the observed violation of the permanence feature. Our findings indicate that, as the material age evolves into the information age, information-exchange behavior has not evolved significantly away from material-exchange behavior.     

It’s Not About You: A Simple Proposition for Improving Biology Education

THE Genetics Society of America’s Elizabeth W. Jones Award for Excellence in Education recognizes significant and sustained impact on genetics education. Consistent with her philosophy of linking research and education, the 2014 Awardee Robin Wright includes undergraduate students in all of her research. She seeks to teach how to think like and to actually be a biologist, working in teams and looking at real-world problems. She emphasizes a learner-centered model of classroom work that promotes and enhances lifelong skills, and has transformed biology education at the University of Minnesota through several efforts including developing the interactive, stimulating Foundations of Biology course sequence, encouraging active learning and open-ended research; supporting the construction of Active Learning Classrooms; and establishing Student Learning Outcomes, standards that measure biology education. She serves as founding editor-in-chief of CourseSource, focusing national effort to collect learner-centered, outcomes-based teaching resources in undergraduate biology.Open in a separate windowRobin Wright     

Is PCR the Next Reference Standard for the Diagnosis of Schistosoma in Stool? A Comparison with Microscopy in Senegal and Kenya

Background

The current reference test for the detection of S. mansoni in endemic areas is stool microscopy based on one or more Kato-Katz stool smears. However, stool microscopy has several shortcomings that greatly affect the efficacy of current schistosomiasis control programs. A highly specific multiplex real-time polymerase chain reaction (PCR) targeting the Schistosoma internal transcriber-spacer-2 sequence (ITS2) was developed by our group a few years ago, but so far this PCR has been applied mostly on urine samples. Here, we performed more in-depth evaluation of the ITS2 PCR as an alternative method to standard microscopy for the detection and quantification of Schistosoma spp. in stool samples.

Methodology/Principal findings

Microscopy and PCR were performed in a Senegalese community (n = 197) in an area with high S. mansoni transmission and co-occurrence of S. haematobium, and in Kenyan schoolchildren (n = 760) from an area with comparatively low S. mansoni transmission. Despite the differences in Schistosoma endemicity the PCR performed very similarly in both areas; 13–15% more infections were detected by PCR when comparing to microscopy of a single stool sample. Even when 2–3 stool samples were used for microscopy, PCR on one stool sample detected more infections, especially in people with light-intensity infections and in children from low-risk schools. The low prevalence of soil-transmitted helminthiasis in both populations was confirmed by an additional multiplex PCR.

Conclusions/Significance

The ITS2-based PCR was more sensitive than standard microscopy in detecting Schistosoma spp. This would be particularly useful for S. mansoni detection in low transmission areas, and post-control settings, and as such improve schistosomiasis control programs, epidemiological research, and quality control of microscopy. Moreover, it can be complemented with other (multiplex real-time) PCRs to detect a wider range of helminths and thus enhance effectiveness of current integrated control and elimination strategies for neglected tropical diseases.     

Fluorescent Treponemal Antibody Tests—A Summary and Comparison

A comparison of current serologic tests for syphilis shows that treponemal tests are preferable to reagin tests in detecting specific antibodies, but that reagin tests are best for determining the response to treatment. The newly developed fta-absorption technique is suggested as a reliable, inexpensive test for treponemal antibodies.     

Comparison of Histological Techniques to Visualize Iron in Paraffin-embedded Brain Tissue of Patients with Alzheimer’s Disease

Better knowledge of the distribution of iron in the brains of Alzheimer’s disease (AD) patients may facilitate the development of an in vivo magnetic resonance (MR) marker for AD and may cast light on the role of this potentially toxic molecule in the pathogenesis of AD. Several histological iron staining techniques have been used in the past but they have not been systematically tested for sensitivity and specificity. This article compares three histochemical techniques and ferritin immunohistochemistry to visualize iron in paraffin-embedded human AD brain tissue. The specificity of the histochemical techniques was tested by staining sections after iron extraction. Iron was demonstrated in the white matter, in layers IV/V of the frontal neocortex, in iron containing plaques, and in microglia. In our hands, these structures were best visualized using the Meguro iron stain, a method that has not been described for iron staining in human brain or AD in particular. Ferritin immunohistochemistry stained microglia and iron containing plaques similar to the Meguro method but was less intense in myelin-associated iron. The Meguro method is most suitable for identifying iron-positive structures in paraffin-embedded human AD brain tissue.     

Single Bacteria Movement Tracking by Online Microscopy – A Proof of Concept Study

In this technical report we demonstrate a low-cost online unit allowing movement tracking of flagellated bacteria on a single-cell level during fermentation processes. The system’s ability to distinguish different metabolic states (viability) of bacteria by movement velocity was investigated. A flow-through cuvette with automatically adjustable layer thickness was developed. The cuvette can be used with most commercially available laboratory microscopes equipped with 40× amplification and a digital camera. In addition, an automated sample preparation unit and a software module was developed measuring size, moved distance, and speed of bacteria. In a proof of principle study the movement velocities of Bacillus amyloliquefaciens FZB42 during three batch fermentation processes were investigated. In this process the bacteria went through different metabolic states, vegetative growth, diauxic shift, vegetative growth after diauxic shift, and sporulation. It was shown that the movement velocities during the different metabolic states significantly differ from each other. Therefore, the described setup has the potential to be used as a bacteria viability monitoring tool. In contrast to some other techniques, such as electro-optical techniques, this method can even be used in turbid production media.     

Cardiac Resuscitation—The Present Status of Defibrillation and Stimulation Techniques

Recent advances in electrical treatment and control of the heart are reviewed. The methods which have evolved for AC and DC countershock defibrillation and arrhythmia correction are outlined, and the parameters defined for determination of the efficacy of treatment.The principal types of cardiac stimulation are described and evaluated in terms of their electrical energy requirements. Externally controlled and implanted stimulators are compared and causes of failure stated.Current developments, reported at a recent Conference on Pacemakers, are included, with a summary of discussions by leading investigators in the field.Studies conducted by the National Research Council (Canada) medical electronics laboratory are also discussed.