scholarly journals A comparison of the Mouse Song Analyzer and DeepSqueak ultrasonic vocalization analysis systems in C57BL/6J, FVB.129, and FVB mice

2021 ◽  
Author(s):  
Matthew S Binder ◽  
Zachary P Pranske ◽  
Joaquin N Lugo
Keyword(s):  
Fundamental Frequency ◽  
Vocal Communication ◽  
Automated Analysis ◽  
Ultrasonic Vocalization ◽  
Ultrasonic Vocalizations ◽  
Automated System ◽  
Two Systems ◽  
Similar Quantity ◽  
Analysis System

Vocal communication is an essential behavior in mammals and is relevant to human neurodevelopmental conditions. Mice produce communicative vocalizations, known as ultrasonic vocalizations (USVs), that can be recorded with various programs. The Mouse Song Analyzer is an automated analysis system, while DeepSqueak is a semi-automated system. We used data from C57BL/6J, FVB.129, and FVB mice to compare whether the DeepSqueak and Mouse Song Analyzer systems measure a similar total number, duration, and fundamental frequency of USVs. We found that the two systems detected a similar quantity of USVs for FVB.129 mice (r= .90, p< .001), but displayed lower correlations for C57BL/6J (r= .76, p< .001) and FVB mice (r= .60, p< .001). We also found that DeepSqueak detected significantly more USVs for C57BL/6J mice than the Mouse Song Analyzer. The two systems detected a similar duration of USVs for C57BL/6J (r= .82, p< .001), but lower correlations for FVB.129 (r= .13, p< .001) and FVB mice (r= .51, p< .01) were found, with DeepSqueak detecting significantly more USVs per each strain. We found lower than acceptable correlations for fundamental frequency in C57BL/6J (r= .54, p< .01), FVB.129 (r= .76, p< .001), and FVB mice (r= .07, p= .76), with the Mouse Song Analyzer detecting a significantly higher fundamental frequency for FVB.129 mice. These findings demonstrate that the strain of mouse used significantly affects the number, duration, and fundamental frequency of USVs that are detected between programs. Overall, we found that DeepSqueak is more accurate than the Mouse Song Analyzer.

scholarly journals Automated Analysis of Fluorescence Microscopy Images to Identify Protein-Protein Interactions

2006 ◽  
Vol 2006 ◽  
pp. 1-10
Author(s):  
S. Venkatraman ◽  
M. J. Doktycz ◽  
H. Qi ◽  
J. L. Morrell-Falvey
Keyword(s):  
Fluorescence Microscopy ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Biological Networks ◽  
Automated Analysis ◽  
Automated System ◽  
Positive Interactions ◽  
Protein Interaction Dataset ◽  
Analysis System ◽  
Microscopy Images

The identification of protein interactions is important for elucidating biological networks. One obstacle in comprehensive interaction studies is the analyses of large datasets, particularly those containing images. Development of an automated system to analyze an image-based protein interaction dataset is needed. Such an analysis system is described here, to automatically extract features from fluorescence microscopy images obtained from a bacterial protein interaction assay. These features are used to relay quantitative values that aid in the automated scoring of positive interactions. Experimental observations indicate that identifying at least 50% positive cells in an image is sufficient to detect a protein interaction. Based on this criterion, the automated system presents 100% accuracy in detecting positive interactions for a dataset of 16 images. Algorithms were implemented using MATLAB and the software developed is available on request from the authors.

scholarly journals A Simple, Flexible, Nonfluorescent System for the Automated Screening of Neurite Outgrowth

2005 ◽  
Vol 11 (2) ◽  
pp. 155-164 ◽  
Author(s):  
Raymond D. Price ◽  
Tomoya Oe ◽  
Takayuki Yamaji ◽  
Nobuya Matsuoka
Keyword(s):  
Neurite Outgrowth ◽  
Kinase Inhibitor ◽  
Rho Kinase ◽  
Automated Analysis ◽  
Automated System ◽  
Neurite Length ◽  
Multiple Parameters ◽  
Neurotrophic Activity ◽  
Automated Screening ◽  
Analysis System

Measurement of neurite outgrowth is a common assay of neurotrophic activity. However, currently available techniques for measuring neurite outgrowth are either time or resource intensive. The authors established a system in which chronic treatment of a subcloned SH-SY5Y cell line with aphidicolin and various concentrations of nerve growth factor (NGF) induced discernable alterations in proliferation and differentiation. Cells were fixed, labeled with a nonfluorescent dye, and evaluated both manually and with an automated analysis system. NGF increased multiple parameters of differentiation, including neurite length, the proportion of cells extending neurites, and branching, as well as promoting cellular survival/proliferation. Interestingly, although NGF treatment increased the total number of branches, it actually decreased the proportion of branches per neurite length. The authors observed no differences in results obtained using the manual and automated systems, but the automated system was orders of magnitude faster. To demonstrate the flexibility of the system, the authors also show that they could measure changes in differentiation induced by a small-molecule Rho kinase inhibitor, as well as by retinoic acid cotreatment with brain-derived neurotrophic factor. In addition to this flexibility, this system does not require specialized equipment or fluorescent antibodies for analysis and therefore provides a less resource-intensive alternative to fluorescence-based systems.

Automated Screening of Neurite Outgrowth

2003 ◽  
Vol 8 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Peter Ramm ◽  
Yuriy Alexandrov ◽  
Andrzej Cholewinski ◽  
Yuriy Cybuch ◽  
Robert Nadon ◽  
...  
Keyword(s):  
Image Analysis ◽  
Automated Analysis ◽  
Automated System ◽  
Neurite Length ◽  
Neurotrophic Activity ◽  
Manual Methods ◽  
Automated Screening ◽  
Analysis System ◽  
Automated Algorithms ◽  
Immunofluorescence Labeling

Outgrowth of neurites in culture is used for assessing neurotrophic activity. Neurite measurements have been performed very slowly using manual methods or more efficiently with interactive image analysis systems. In contrast, medium-throughput and noninteractive image analysis of neurite screens has not been well described. The authors report the performance of an automated image acquisition and analysis system (IN Cell Analyzer 1000) in the neurite assay. Neuro-2a (N2a) cells were plated in 96-well plates and were exposed to 6 conditions of retinoic acid. Immunofluorescence labeling of the cytoskeleton was used to detect neurites and cell bodies. Acquisition of the images was automatic. The image set was then analyzed by both manual tracing and automated algorithms. On 5 relevant parameters (number of neurites, neurite length, total cell area, number of cells, neurite length per cell), the authors did not observe a difference between the automated analysis and the manual analysis done by tracing. These data suggest that the automated system addresses the same biology as human scorers and with the same measurement precision for treatment effects. However, throughput of the automated system is orders of magnitude higher than with manual methods. ( Journal of Biomolecular Screening 2003:7-18)

The Ontogeny of Ultrasonic Vocalization in Microtus Montanus

Behaviour ◽  
1977 ◽  
Vol 60 (1-2) ◽  
pp. 115-121 ◽  
Author(s):  
V.J. De Ghett
Keyword(s):  
Short Duration ◽  
Maternal Care ◽  
Ultrasonic Vocalization ◽  
Ultrasonic Vocalizations ◽  
Developmental Changes ◽  
Maternal Behaviour ◽  
Postnatal Ontogeny ◽  
Microtus Montanus ◽  
Early Peak ◽  
The Mean

AbstractDevelopmental changes in parameters of ultrasound production were investigated in M. montanus young. The rate of ultrasonic vocalization reached a peak on Day 2 of postnatal ontogeny and declined to zero on Day 15. A similar developmental pattern has been found in several other rodent species. However, the comparatively early peak rate is indicative of a degree of ontogenic precociousness. Other developmental changes, both behavioural and morphological, tend to confirm that M. montanus young are relatively precocious. The duration of ultrasonic vocalizations did not show a significant change across early development. The mean duration for each vocalization sampled was 22.92 msec. The distribution of these vocalizations showed that a considerable number of vocalizations were of very short duration (<30 msec). The developmental changes in the percentage of young emitting ultrasounds began to decline following Day 8 and reached zero percent on Day 15. This decline in the percentage of young vocalizing corresponded to changes in maternal behaviour. Both the rate of ultrasonic vocalization and the percentage of young vocalizing were significantly correlated with the age of the young. Being correlated with age, these parameters of ultrasound production have the possibility of having great communicative value for the purposes of maternal care.

Automated Extraction and Presentation of Data Practices in Privacy Policies

2021 ◽  
Vol 2021 (2) ◽  
pp. 88-110
Author(s):  
Duc Bui ◽  
Kang G. Shin ◽  
Jong-Min Choi ◽  
Junbum Shin
Keyword(s):  
User Study ◽  
Personal Information ◽  
Personal Data ◽  
Neural Model ◽  
Automated Analysis ◽  
Entity Recognition ◽  
Automated System ◽  
Privacy Policies ◽  
Fine Grained ◽  
Data Practices

Abstract Privacy policies are documents required by law and regulations that notify users of the collection, use, and sharing of their personal information on services or applications. While the extraction of personal data objects and their usage thereon is one of the fundamental steps in their automated analysis, it remains challenging due to the complex policy statements written in legal (vague) language. Prior work is limited by small/generated datasets and manually created rules. We formulate the extraction of fine-grained personal data phrases and the corresponding data collection or sharing practices as a sequence-labeling problem that can be solved by an entity-recognition model. We create a large dataset with 4.1k sentences (97k tokens) and 2.6k annotated fine-grained data practices from 30 real-world privacy policies to train and evaluate neural networks. We present a fully automated system, called PI-Extract, which accurately extracts privacy practices by a neural model and outperforms, by a large margin, strong rule-based baselines. We conduct a user study on the effects of data practice annotation which highlights and describes the data practices extracted by PI-Extract to help users better understand privacy-policy documents. Our experimental evaluation results show that the annotation significantly improves the users’ reading comprehension of policy texts, as indicated by a 26.6% increase in the average total reading score.

scholarly journals Field Propagation Experiments of Male African Savanna Elephant Rumbles: A Focus on the Transmission of Formant Frequencies

Animals ◽  
2018 ◽  
Vol 8 (10) ◽  
pp. 167 ◽  
Author(s):  
Anton Baotic ◽  
Maxime Garcia ◽  
Markus Boeckle ◽  
Angela Stoeger
Keyword(s):  
Fundamental Frequency ◽  
Vocal Communication ◽  
Vocal Tract ◽  
Natural Habitat ◽  
Ecological Factors ◽  
Transmission Efficiency ◽  
Long Distance ◽  
African Savanna ◽  
Formant Frequencies ◽  
Resonance Frequencies

African savanna elephants live in dynamic fission–fusion societies and exhibit a sophisticated vocal communication system. Their most frequent call-type is the ‘rumble’, with a fundamental frequency (which refers to the lowest vocal fold vibration rate when producing a vocalization) near or in the infrasonic range. Rumbles are used in a wide variety of behavioral contexts, for short- and long-distance communication, and convey contextual and physical information. For example, maturity (age and size) is encoded in male rumbles by formant frequencies (the resonance frequencies of the vocal tract), having the most informative power. As sound propagates, however, its spectral and temporal structures degrade progressively. Our study used manipulated and resynthesized male social rumbles to simulate large and small individuals (based on different formant values) to quantify whether this phenotypic information efficiently transmits over long distances. To examine transmission efficiency and the potential influences of ecological factors, we broadcasted and re-recorded rumbles at distances of up to 1.5 km in two different habitats at the Addo Elephant National Park, South Africa. Our results show that rumbles were affected by spectral–temporal degradation over distance. Interestingly and unlike previous findings, the transmission of formants was better than that of the fundamental frequency. Our findings demonstrate the importance of formant frequencies for the efficiency of rumble propagation and the transmission of information content in a savanna elephant’s natural habitat.

Automated Analysis of Organophosphorus Insecticides by Wet Digestion-Oxidation and Colorimetric Determination of the Derived Orthophosphate

1968 ◽  
Vol 51 (3) ◽  
pp. 697-708
Author(s):  
Daniel E Ott ◽  
Francis A Gunther
Keyword(s):  
Thin Layer ◽  
Automated Analysis ◽  
Automated System ◽  
Phosphorus Compounds ◽  
Colorimetric Determination ◽  
Total System ◽  
Blue Color ◽  
Automated Technique ◽  
Analytical System

Abstract Adaptation of an AutoAnalyzer system to the determination of phosphorus in organic compounds now provides an automated technique generally applicable for the analysis of organophosphorus inserticides. Following automated wet digestionoxidation of the compounds (some need preliminary alkaline hydrolysis) the resulting orthophosphate is determined automatically by a colorimetric system reading a phosphomolybdenum blue color at 815 mμ. The total system handles 10 samples per hour with a precision and sensitivity readily practical for organophosphorus insecticide analysis; the insecticidal solutions tested, at concentrations of 2 μg/ml or greater, gave repeatable responses within ± 10%. Manual cleanup procedures for most crop samples are required to remove interfering noninsecticidal phosphorus compounds before the system is applicable to total residue analyses. Thimet (phorate) and phosphamidon at 0.5 ppm in fortified stripping solutions of strawberries were analyzed separately without cleanup, however. Adsorption column chromatography on Florisil has provided rapid and efficient cleanup of fortified spinach extractives prior to automated analysis of Thimet and dimethoate. Autoanalysis of individual spots from thin layer chromatograms provides considerable specificity to this nonspecific analytical system, and for some crops provides all the cleanup necessary. Thin layer "spots" can be introduced directly into the automated system.

Results of the automated analysis of 328 bladder specimens using the Leyden television analysis system (LEYTAS)

1983 ◽  
Vol 1 (2) ◽  
pp. 77-81 ◽  
Author(s):  
H. J. Tanke ◽  
J. A. M. Brussee ◽  
A. M. J. van Driel-Kulker ◽  
M. J. van der Burg ◽  
C. F. H. M. Schelvis-Knepfle ◽  
...  
Keyword(s):  
Automated Analysis ◽  
Analysis System
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