On the Contribution of Binocular Disparity to the Long-Term Memory for Natural Scenes

Binocular disparity is a fundamental dimension defining the input we receive from the visual world, along with luminance and chromaticity. In a memory task involving images of natural scenes we investigate whether binocular disparity enhances long-term visual memory. We found that forest images studied in the presence of disparity for relatively long times (7s) were remembered better as compared to 2D presentation. This enhancement was not evident for other categories of pictures, such as images containing cars and houses, which are mostly identified by the presence of distinctive artifacts rather than by their spatial layout. Evidence from a further experiment indicates that observers do not retain a trace of stereo presentation in long-term memory.     

Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology

The extraction of accurate self-motion information from the visual world is a difficult problem that has been solved very efficiently by biological organisms utilizing non-linear processing. Previous bio-inspired models for motion detection based on a correlation mechanism have been dogged by issues that arise from their sensitivity to undesired properties of the image, such as contrast, which vary widely between images. Here we present a model with multiple levels of non-linear dynamic adaptive components based directly on the known or suspected responses of neurons within the visual motion pathway of the fly brain. By testing the model under realistic high-dynamic range conditions we show that the addition of these elements makes the motion detection model robust across a large variety of images, velocities and accelerations. Furthermore the performance of the entire system is more than the incremental improvements offered by the individual components, indicating beneficial non-linear interactions between processing stages. The algorithms underlying the model can be implemented in either digital or analog hardware, including neuromorphic analog VLSI, but defy an analytical solution due to their dynamic non-linear operation. The successful application of this algorithm has applications in the development of miniature autonomous systems in defense and civilian roles, including robotics, miniature unmanned aerial vehicles and collision avoidance sensors.     

Visualizing the Topical Structure of the Medical Sciences: A Self-Organizing Map Approach

Background

We implement a high-resolution visualization of the medical knowledge domain using the self-organizing map (SOM) method, based on a corpus of over two million publications. While self-organizing maps have been used for document visualization for some time, (1) little is known about how to deal with truly large document collections in conjunction with a large number of SOM neurons, (2) post-training geometric and semiotic transformations of the SOM tend to be limited, and (3) no user studies have been conducted with domain experts to validate the utility and readability of the resulting visualizations. Our study makes key contributions to all of these issues.

Methodology

Documents extracted from Medline and Scopus are analyzed on the basis of indexer-assigned MeSH terms. Initial dimensionality is reduced to include only the top 10% most frequent terms and the resulting document vectors are then used to train a large SOM consisting of over 75,000 neurons. The resulting two-dimensional model of the high-dimensional input space is then transformed into a large-format map by using geographic information system (GIS) techniques and cartographic design principles. This map is then annotated and evaluated by ten experts stemming from the biomedical and other domains.

Conclusions

Study results demonstrate that it is possible to transform a very large document corpus into a map that is visually engaging and conceptually stimulating to subject experts from both inside and outside of the particular knowledge domain. The challenges of dealing with a truly large corpus come to the fore and require embracing parallelization and use of supercomputing resources to solve otherwise intractable computational tasks. Among the envisaged future efforts are the creation of a highly interactive interface and the elaboration of the notion of this map of medicine acting as a base map, onto which other knowledge artifacts could be overlaid.     

A Site-Specific Approach for the Evaluation of Natural Attenuation at Metals-Impacted Sites

Consideration of monitored natural attenuation (MNA) as a remedy component for metals-contaminated sites can be achieved using a site-specific screening approach, followed by application of one or a series of sequential extraction measurements. Hazardous waste sites contaminated with metals can be screened for the implementation of monitored natural attenuation on the basis of contaminant-specific soil chemical characteristics (i.e., K_d's, solubilities, and nonexchangeable sorbed fraction). Field cases are used to demonstrate the screening approach and to outline the primary considerations involved in accurately applying sequential extraction procedures to support the of MNA for site remediation. The results of these case studies provide strong evidence that site-specific screening and the use of sequential extraction procedures are effective methods for evaluating natural attenuation for metals impacted sites.     

A Method for Visualizing the Acrosome by Light Microscopy

A silver staining technique applied to squash preparations of material previously fixed in 3:1 ethanol: acetic acid produces differential staining of the acrosomal region of spermatids during spermiogenesis in orthopteroid species. The method includes treatment with saline sodium citrate solution for 15 min at 60 C, and staining with 50% aqueous silver nitrate adjusted to pH 2.9 with formic acid.     

Preliminary Biomechanical Study of Different Acetabular Reinforcement Devices for Acetabular Reconstruction

Background

Acetabular reinforcement devices (ARDs) are frequently used as load-sharing devices to allow allograft incorporation in revision hip arthroplasty with massive acetabular bone loss. The key to a successful reconstruction is robust fixation of the device to the host acetabulum. Interlocking fixation is expected to improve the initial stability of the postoperative construct. However, all commercially available ARDs are designed with non-locking fixation. This study investigates the efficacy of standard ARDs modified with locking screw mechanisms for improving stability in acetabular reconstruction.

Methods

Three types of ARDs were examined to evaluate the postoperative compression and angular stability: i) standard commercial ARDs, ii) standard ARDs modified with monoaxial and iii) standard ARDs modified with polyaxial locking screw mechanisms. All ARDs were implanted into osteomized synthetic pelvis with pelvic discontinuity. Axial compression and torsion tests were then performed using a servohydraulic material testing machine that measured load (angle) versus displacement (torque). Initial stability was compared among the groups.

Results

Equipping ARDs with interlocking mechanisms effectively improved the initial stability at the device/bone interface compared to standard non-locked ARDs. In both compression and torsion experiments, the monoaxial interlocking construct demonstrated the highest construct stiffness (672.6 ± 84.1 N/mm in compression and 13.3 ± 1.0 N·m/degree in torsion), whereas the non-locked construct had the lowest construct stiffness (381.4 ± 117.2 N/mm in compression and 6.9 ± 2.1 N·m/degree in torsion) (P < 0.05).

Conclusions

Our study demonstrates the potential benefit of adding a locking mechanism to an ARD. Polyaxial ARDs provide the surgeon with more flexibility in placing the screws at the cost of reduced mechanical performance. This in vitro study provides a preliminary evaluation of biomechanical performance for ARDs with or without interlocking mechanisms, actual clinical trial deserves to be further investigated in future studies.     

Are We all Natural Dualists? A Cognitive Developmental Approach*

The article takes to task the well-established anthropological claim that non-Western peoples are free from the traps of dualistic thinking. Although Vezo informants in Madagascar produce statements that could be used to support such a claim, experimental procedures that target their inferential reasoning reveal that they systematically differentiate between mind and body, between the biological processes that determine the organism and the social processes that shape personhood. This suggests that there is a significant discrepancy between people's explicit linguistic statements and their implicit theoretical knowledge. Moreover, developmental data show that such implicit theoretical presuppositions are essential to the production and transmission of cultural knowledge. Thus, Vezo children, who do not as yet differentiate between the biological mechanism of birth and the social mechanism of nurture, are still unable to grasp a salient aspect of Vezo culture, namely the causally integrated set of ideas that guide the way adults classify the social world. These findings have significant theoretical and methodological implications for the constitution of anthropological knowledge.     

Novel Approach to Simulate Sleep Apnea Patients for Evaluating Positive Pressure Therapy Devices

Bench testing is a useful method to characterize the response of different automatic positive airway pressure (APAP) devices under well-controlled conditions. However, previous models did not consider the diversity of obstructive sleep apnea (OSA) patients’ characteristics and phenotypes. The objective of this proof-of-concept study was to design a new bench test for realistically simulating an OSA patient’s night, and to implement a one-night example of a typical female phenotype for comparing responses to several currently-available APAP devices. We developed a novel approach aimed at replicating a typical night of sleep which includes different disturbed breathing events, disease severities, sleep/wake phases, body postures and respiratory artefacts. The simulated female OSA patient example that we implemented included periods of wake, light sleep and deep sleep with positional changes and was connected to ten different APAP devices. Flow and pressure readings were recorded; each device was tested twice. The new approach for simulating female OSA patients effectively combined a wide variety of disturbed breathing patterns to mimic the response of a predefined patient type. There were marked differences in response between devices; only three were able to overcome flow limitation to normalize breathing, and only five devices were associated with a residual apnea-hypopnea index of <5/h. In conclusion, bench tests can be designed to simulate specific patient characteristics, and typical stages of sleep, body position, and wake. Each APAP device behaved differently when exposed to this controlled model of a female OSA patient, and should lead to further understanding of OSA treatment.     

An Approach for Adaptive Limbless Locomotion Using a CPG-Based Reflex Mechanism

Animals＇ free movement in natural environments has attracted many researchers to explore control methods for bio-inspired robots. This paper presents a novel reflex mechanism based on a Central Pattern Generator （CPG） for adaptive locomotion of limbless robots. First, inspired by the concept of reflex arc, the reflex mechanism is designed on a connectionist CPG model. Since the CPG model inspired by the spinal cord of lampreys is developed at the neuron level, it provides a possible natural solution for sensory reflex integration. Therefore, sensory neurons that bridge the external stimuli and the CPG model, together with the concept of reflex arc, are utilized for designing the sensory reflex mechanism. Then, a border reflex and a body reflex are further developed and applied on the ends and the middle part of a limbless robot, respectively. Finally, a ball hitting scenario and a corridor passing scenario are designed to verify the proposed method. Results of simulations and on-site experiments show the feasibility and effectiveness of the reflex mechanism in realizing fast response and adaptive limbless locomotion.     

A New Fluorescence Staining Assay for Visualizing Living Microorganisms in Soil

5- (and 6-)Sulfofluorescein diacetate (SFDA), which is converted to a fluorescent product by intracellular esterase activity, was used to stain living microorganisms, including bacteria, Saccharomyces cerevisiae, and fungi, in soil. SFDA (1 mM) dissolved in ethyl alcohol was added to an intact soil sample, and the preparation was examined with an epifluorescence microscope. Bright single cells and colonies of live bacteria were observed without interference from the autofluorescence of soil minerals and detritus. Cultured Escherichia coli was killed through heat treatment; thus, SFDA was concluded to stain only living cells. Microbial colonies obtained from natural soils and various cultured strains were tested. It was found that 151 of 154 colonies from natural soils were stained and that hyphae and spores from 1 of 28 cultured microbial strains were not stained. The SFDA method was successfully used to visualize and count bacteria in soil samples from Mount Shiga in Japan.     

SOMEViz: A Web Service for Site of Metabolism Estimating and Visualizing

Phase I metabolism is an important consideration in drug discovery because it profoundly affects the toxicity and activity profile of a drug candidate. In these metabolic processes, CYP450 family is responsible for the majority of biotransformation events. However, it is still an important challenge to predict sites of metabolism (SOM) of a new chemical entity due to the complex reaction mechanism and variety in CYP450 enzymes. SOMEViz is an online service designed for predicting and visualizing human cytochromes P450 (CYP450)-mediated sites of metabolism (SOM) of a molecule, on the basis of a previously reported model [1]. The service provides an access for predicting sites of metabolism of molecules with reasonable accuracy, and predicted results are shown in a user-friendly as well as interactive way, which may help chemists explore metabolism properties of chemicals in the early stage of drug discovery. The web-based GUI of SOMEViz offers user a straightforward way to manage and visualize the sites of metabolism (SOM) prediction results. The service and examples are available free of charge at http://www.dddc.ac.cn/some.     

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

This is a PLOS Computational Biology Software paper.

     

A Forensically Sound Adversary Model for Mobile Devices

In this paper, we propose an adversary model to facilitate forensic investigations of mobile devices (e.g. Android, iOS and Windows smartphones) that can be readily adapted to the latest mobile device technologies. This is essential given the ongoing and rapidly changing nature of mobile device technologies. An integral principle and significant constraint upon forensic practitioners is that of forensic soundness. Our adversary model specifically considers and integrates the constraints of forensic soundness on the adversary, in our case, a forensic practitioner. One construction of the adversary model is an evidence collection and analysis methodology for Android devices. Using the methodology with six popular cloud apps, we were successful in extracting various information of forensic interest in both the external and internal storage of the mobile device.     

A Novel Approach Toward Natural and Anthropogenic Risk Assessment of Gas Power Plants

The current study focuses on identification and prioritization of the most important risks affecting a gas power plant located in southern Iran that was selected as a case study. After identifying risky activities, plant operations, and natural disasters, a Delphi questionnaire was prepared to specify crisis and accident-prone centers that could lead to the plant's destruction. After analyzing the questionnaires, the final criteria were determined. Subsequently, multi-criteria decision-making methods including technique for order preference by similarity to ideal solution (TOPSIS) and analytical hierarchy process (AHP) were applied to prioritize the identified criteria. The relative weights of the criteria were calculated using the eigenvector method in the environment of MATLAB and EXPERT CHOICE. In some cases, there was no correlation between the obtained results, resulting in a novel integrated technique consisting of three methods: average, Borda, and Copeland was used to reach a consensus for prioritizing the criteria. The risk assessment results indicate that gas and oil pipes, dust storm, and terrorism have the first to third priorities among the other risks. Some strategies are proposed to control and mitigate the identified risks.     

A New Approach Toward Natural and Anthropogenic Risk Assessment of Gas Power Plants

The current study focuses on identification and prioritization of the most important risks affecting a gas power plant located in southern Iran that was selected as a case study. After identifying risky activities, plant operations, and natural disasters, a Delphi questionnaire was prepared to specify crisis and accident-prone centers that could lead to the plant's destruction. After analyzing the questionnaires, the final criteria were determined. Subsequently, multi-criteria decision-making methods including the technique for order preference by similarity to ideal solution (TOPSIS) and analytical hierarchy process (AHP) were applied to prioritize the identified criteria. The relative weights of the criteria were calculated using the eigenvector method in the environment of MATLAB and Expert Choice. In some cases, there was no correlation between the obtained results, resulting in a novel integrated technique consisting of three methods: average, Borda, and Copeland were used to reach a consensus for prioritizing the criteria. The risk assessment results indicate that gas and oil pipes, dust storm, and terrorism have the first to third priorities among the other risks. Some strategies are proposed to control and mitigate the identified risks.     

乌兰布和沙漠天然白刺适应性群团抽样技术的研究

以乌兰布和沙漠地区天然白刺为具体研究对象,对不同抽样方法获取的数据进行了分析.研究结果表明,当适应性标准大于等于占位单元平均数时,适应性群团抽样比简单随机抽样更有效,并且可以保证估计精度;初始抽样比例越大,总体均值估计值和抽样相对效率越稳定.在该研究区域采用二阶适应性群团抽样,可以达到估计精度,但与简单随机抽样和适应性群团抽样相比效率偏低.