scholarly journals SIANN: Strain Identification by Alignment to Near Neighbors

2014 ◽  
Author(s):  
Samuel Minot ◽  
Stephen D Turner ◽  
Krista L Ternus ◽  
Dana R Kadavy
Keyword(s):  
State Of The Art ◽  
Clinical Applications ◽  
Near Neighbor ◽  
Strain Identification ◽  
Strain Specificity ◽  
Mixed Sample ◽  
Current State ◽  
High Positive Predictive Value ◽  
High Degree ◽  
Generation Sequencing

Next-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifically designed to rapidly detect a set of target organisms in mixed samples that achieves a high degree of species- and strain-specificity by aligning short sequence reads to the genomes of near neighbor organisms, as well as that of the target. Empirical benchmarking alongside the current state-of-the-art methods shows an extremely high Positive Predictive Value, even at very low abundances of the target organism in a mixed sample. SIANN is available as an Illumina BaseSpace app, as well as through Signature Science, LLC. SIANN results are presented in a streamlined report designed to be comprehensible to the non-specialist user, providing a powerful tool for rapid species detection in a mixed sample. By focusing on a set of (customizable) target organisms and their near neighbors, SIANN can operate quickly and with low computational requirements while delivering highly accurate results.

You Need Teachers

PEDIATRICS ◽  
1979 ◽  
Vol 64 (1) ◽  
pp. 125-125
Author(s):  
Miles Weinberger
Keyword(s):  
State Of The Art ◽  
Review Article ◽  
Current State ◽  
Children With Asthma ◽  
Degree Of Control ◽  
Considerable Morbidity ◽  
High Degree ◽  
Changing Role ◽  
Excellent Review Article

The excellent review article by Leffert1 and the accompanying commentary by Bergner2 made important points regarding the changing role of the pediatric allergist and the broad requirements for knowledge of any physicians who are to provide specialty care for children with asthma. While the current state of the art allows a high degree of control for this disease,3 considerable morbidity from inadequately treated asthma persists. This situation is unlikely to change rapidly unless departments of pediatrics place a high priority on ensuring that the modern allergist described by Dr. Bergner is on their faculty to teach the current housestaff and provide continuing education for the practitioner; only then will most general pediatricians be able to assume the role envisioned by Dr. Leffert.

scholarly journals Magnetotactic Bacteria and Magnetosomes: Basic Properties and Applications

2021 ◽  
Vol 7 (6) ◽  
pp. 86
Author(s):  
Kamil G. Gareev ◽  
Denis S. Grouzdev ◽  
Petr V. Kharitonskii ◽  
Andrei Kosterov ◽  
Veronika V. Koziaeva ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Biomedical Applications ◽  
State Of The Art ◽  
Rock Magnetism ◽  
Magnetotactic Bacteria ◽  
Resonance Imaging ◽  
Current State ◽  
Magnetite Fe3o4 ◽  
High Degree ◽  
Potential Use

Magnetotactic bacteria (MTB) belong to several phyla. This class of microorganisms exhibits the ability of magneto-aerotaxis. MTB synthesize biominerals in organelle-like structures called magnetosomes, which contain single-domain crystals of magnetite (Fe3O4) or greigite (Fe3S4) characterized by a high degree of structural and compositional perfection. Magnetosomes from dead MTB could be preserved in sediments (called fossil magnetosomes or magnetofossils). Under certain conditions, magnetofossils are capable of retaining their remanence for millions of years. This accounts for the growing interest in MTB and magnetofossils in paleo- and rock magnetism and in a wider field of biogeoscience. At the same time, high biocompatibility of magnetosomes makes possible their potential use in biomedical applications, including magnetic resonance imaging, hyperthermia, magnetically guided drug delivery, and immunomagnetic analysis. In this review, we attempt to summarize the current state of the art in the field of MTB research and applications.

scholarly journals Interpretable Machine Learning for Genomics

2021 ◽  
Author(s):  
David Watson
Keyword(s):  
Machine Learning ◽  
Cell Function ◽  
State Of The Art ◽  
Future Research ◽  
Computational Statistics ◽  
Close Collaboration ◽  
Current State ◽  
Interpretable Machine Learning ◽  
Underlying Mechanisms ◽  
Generation Sequencing

Abstract High-throughput technologies such as next generation sequencing allow biologists to observe cell function with unprecedented resolution, but the resulting datasets are too large and complicated for humans to understand without the aid of advanced statistical methods. Machine learning (ML) algorithms, which are designed to automatically find patterns in data, are well suited to this task. Yet these models are often so complex as to be opaque, leaving researchers with few clues about underlying mechanisms. Interpretable machine learning (iML) is a burgeoning subdiscipline of computational statistics devoted to making the predictions of ML models more intelligible to end users. This article is a gentle and critical introduction to iML, with an emphasis on genomic applications. I define relevant concepts, motivate leading methodologies, and provide a simple typology of existing approaches. I survey recent examples of iML in genomics, demonstrating how such techniques are increasingly integrated into research workflows. I argue that iML solutions are required to realize the promise of precision medicine. However, several open challenges remain. I examine the limitations of current state of the art tools and propose a number of directions for future research. While the horizon for iML in genomics is wide and bright, continued progress requires close collaboration across disciplines.

scholarly journals Whey: State of the Art. Part II. Processes and Treatment Methods

2021 ◽  
Vol 57 (3) ◽  
pp. 83-101
Author(s):  
I. Paladii ◽  
◽  
Е. Vrabie ◽  
C. Sprincean ◽  
Mircea Bologa ◽  
...  
Keyword(s):  
State Of The Art ◽  
Anaerobic Fermentation ◽  
Selective Adsorption ◽  
Whey Proteins ◽  
Electrochemical Activation ◽  
Labor Costs ◽  
Processing Methods ◽  
Current State ◽  
Membrane Processing ◽  
High Degree

The current state of the art on studying of whey is considered. The processes and methods of whey processing (thermal, chemical, physicochemical, biotechnological, and electrophysical) are presented. Thermal and isoelectric precipitation of proteins, using reagents and coagulants, as well as the main membrane processing methods (reverse osmosis, diafiltration, microfiltration, ultrafiltration, and nanofiltration) are described. Possibi-lities of effective separation of whey proteins by a combination of membrane and other methods are noted. Chromatographic methods for fractionation of whey proteins (chromatography with imitation of a moving bed, high-gradient chromatography with a magnetic trap, selective adsorption, displacement chromatography, membrane adsorption), which provide a high degree of separation, are described. Highly porous chromatographic materials providing a high flow rate, biotechnological processing methods – biosynthesis of lactulose, enzymatic hydrolysis of lactose and whey proteins, aerobic and anaerobic fermentation are considered. Electrophysical methods of processing whey (electrodialysis, electroactivation), which include electrodialysis and electro-activation, as well as electrochemical activation as a phenomenon and technology, as a new promising processing method that allows to create a waste-free cycle for obtaining valuable components and useful derivatives from whey without the use of reagents are analyzed. It is emphasized that, depending on the regimes used, protein-mineral concentrates with a predetermined protein or mineral composition are obtained with the simultaneous isomerization of lactose into lactulose. It is stated that the efficiency of methods for processing whey is ensured by a significant increase in the efficiency of technological processes, a decrease in labor costs, a reduction in the processing time and materials, and an improvement in the quality and functional properties of the final products.

scholarly journals Using Social Signals to Predict Shoplifting: A Transparent Approach to a Sensitive Activity Analysis Problem

Sensors ◽  
2021 ◽  
Vol 21 (20) ◽  
pp. 6812
Author(s):  
Shane Reid ◽  
Sonya Coleman ◽  
Philip Vance ◽  
Dermot Kerr ◽  
Siobhan O’Neill
Keyword(s):  
Signal Processing ◽  
State Of The Art ◽  
High Accuracy ◽  
Black Box ◽  
Social Signals ◽  
Social Signal Processing ◽  
Legal Cases ◽  
Current State ◽  
Social Signal ◽  
High Degree

Retail shoplifting is one of the most prevalent forms of theft and has accounted for over one billion GBP in losses for UK retailers in 2018. An automated approach to detecting behaviours associated with shoplifting using surveillance footage could help reduce these losses. Until recently, most state-of-the-art vision-based approaches to this problem have relied heavily on the use of black box deep learning models. While these models have been shown to achieve very high accuracy, this lack of understanding on how decisions are made raises concerns about potential bias in the models. This limits the ability of retailers to implement these solutions, as several high-profile legal cases have recently ruled that evidence taken from these black box methods is inadmissible in court. There is an urgent need to develop models which can achieve high accuracy while providing the necessary transparency. One way to alleviate this problem is through the use of social signal processing to add a layer of understanding in the development of transparent models for this task. To this end, we present a social signal processing model for the problem of shoplifting prediction which has been trained and validated using a novel dataset of manually annotated shoplifting videos. The resulting model provides a high degree of understanding and achieves accuracy comparable with current state of the art black box methods.

The Future of CMP

MRS Bulletin ◽  
2002 ◽  
Vol 27 (10) ◽  
pp. 779-783 ◽  
Author(s):  
David Evans
Keyword(s):  
Noble Metals ◽  
Silicon Oxide ◽  
State Of The Art ◽  
Electronic Devices ◽  
Advanced Materials ◽  
Mixed Metal Oxide ◽  
Current State ◽  
Microfabrication Technology ◽  
High Degree ◽  
Silicon Silicon

AbstractChemical–mechanical polishing, or planarization (CMP), is one of several advanced microfabrication processes that provide complementary capabilities for constructing advanced electronic devices. At the current state of the art, CMP demonstrates significant advantages due to its high degree of process flexibility, particularly in the chemical formulation of polishing solutions and slurries. This article explores some possible future applications of CMP using new advanced materials other than silicon, silicon oxide, and silicon nitride. Such materials may include refractory and noble metals, high-κ insulators, and mixed metal oxide perovskites. Although no one can predict future applications with absolute certainty, it seems safe to conclude that CMP will remain a key microfabrication technology for the foreseeable future.

Computer Support in the Design and Testing of Undersea Towed Systems

1974 ◽  
Vol 11 (02) ◽  
pp. 159-172
Author(s):  
John D. Burroughs ◽  
Raymond C. Benz
Keyword(s):  
System Analysis ◽  
State Of The Art ◽  
Equations Of Motion ◽  
Computer Support ◽  
Current State ◽  
Engineering Problems ◽  
Practical Engineering ◽  
High Degree ◽  
Design And Testing ◽  
Made In

Since 1965 the authors' company has developed, assembled, and applied a computer simulation to the problem of analyzing the static and dynamic behavior of underwater towed systems. As a result of a recent survey [16]3 of towed system dynamic analysis literature, it became apparent that other investigators in the field of towed system analysis were either completely unaware of this work or had only a very superficial knowledge of it. It is a purpose of this paper to describe the modeling approach taken for the towed system and to present the methods used to derive the equations of motion for the model. Assumptions that were made in order to achieve practical solutions to the equations of motion also are discussed. A high degree of correlation with actual towing trials has been achieved by this analysis and it has been demonstrated that practical engineering problems can be solved using such a simulation tool. The computer support provided in 1970 to underway sea trials of a hydrofoil towed system is presented and discussed. It is believed that this simulation represents the current state of the art in towed system simulation.

scholarly journals We are not ready yet: limitations of transfer learning for Disease Named Entity Recognition

2021 ◽  
Author(s):  
Lisa Langnickel ◽  
Juliane Fluck
Keyword(s):  
Transfer Learning ◽  
Language Processing ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Clinical Applications ◽  
Entity Recognition ◽  
Data Sets ◽  
Named Entity ◽  
Current State ◽  
Biomedical Named Entity Recognition

Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical applications. For the available data sets, these models show excellent results - partly exceeding the inter-annotator agreements. However, biomedical named entity recognition applied on COVID-19 preprints shows a performance drop compared to the results on available test data. The question arises how well trained models are able to predict on completely new data, i.e. to generalize. Based on the example of disease named entity recognition, we investigate the robustness of different machine learning-based methods - thereof transfer learning - and show that current state-of-the-art methods work well for a given training and the corresponding test set but experience a significant lack of generalization when applying to new data. We therefore argue that there is a need for larger annotated data sets for training and testing.

Behavioral Genetics: Concepts for Research and Practice in Language Development and Disorders

1995 ◽  
Vol 38 (5) ◽  
pp. 1126-1142 ◽  
Author(s):  
Jeffrey W. Gilger
Keyword(s):  
Language Development ◽  
Behavioral Genetics ◽  
State Of The Art ◽  
Genetic Research ◽  
Great Promise ◽  
Behavioral Genetic ◽  
Fine Grained ◽  
Future Goals ◽  
Current State ◽  
Research Designs

This paper is an introduction to behavioral genetics for researchers and practioners in language development and disorders. The specific aims are to illustrate some essential concepts and to show how behavioral genetic research can be applied to the language sciences. Past genetic research on language-related traits has tended to focus on simple etiology (i.e., the heritability or familiality of language skills). The current state of the art, however, suggests that great promise lies in addressing more complex questions through behavioral genetic paradigms. In terms of future goals it is suggested that: (a) more behavioral genetic work of all types should be done—including replications and expansions of preliminary studies already in print; (b) work should focus on fine-grained, theory-based phenotypes with research designs that can address complex questions in language development; and (c) work in this area should utilize a variety of samples and methods (e.g., twin and family samples, heritability and segregation analyses, linkage and association tests, etc.).

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