Biobrick chain recommendations for genetic circuit design
Synthetic biology databases have collected numerous biobricks to accelerate genetic circuit design. However, selecting biobricks is a tough task. Here, we leverage the fact that these manually designed circuits can provide underlying knowledge to support biobrick selection. We propose to design a recommendation system based on the analysis of available genetic circuits, which can narrow down the biobrick selection range and provide candidate biobricks for users to choose. A recommendation strategy based on a Markov model is established to tackle this issue. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - May 2, 2017 Category: Bioinformatics Authors: Jiaoyun Yang, Song Yu, Bowen Gong, Ning An, Gil Alterovitz Source Type: research
Numerical study on the air conditioning characteristics of the human nasal cavity
The air-conditioning characteristics of the human nasal cavity were investigated using computational fluid dynamics. The wall layer was modeled as a heat conducting layer consisting of water with constant thickness placed on top of epithelial cells. By assuming constant tissue temperature, prescribed to be 36 °C, which is close to the alveolar condition, the proposed wall model yielded a spatially varying surface temperature distribution that is in reasonable agreement with the measurement studies in the literature. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 30, 2017 Category: Bioinformatics Authors: Da-Woon Kim, Seung-Kyu Chung, Yang Na Source Type: research
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(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 28, 2017 Category: Bioinformatics Source Type: research
A robust construction algorithm of the centerline skeleton for complex aortic vascular structure using computational fluid dynamics
Centerlines of blood vessels are useful tools to make important anatomical measurements (length, diameter, area), which cannot be accurately obtained using 2D images. In this paper a brand new method for centerline extraction of vascular trees is presented. By using computational fluid dynamics (CFD) we are able to obtain a robust and purely functional centerline allowing us to support better measurements than classic purely geometrical-based centerlines. We show that the CFD-based centerline is within a few pixels from the geometrical centerline where the latter is defined (far away from inlet/outlets and from the branche...
Source: Computers in Biology and Medicine - April 28, 2017 Category: Bioinformatics Authors: Joulien Touati, Marco Bologna, Adeline Schwein, Francesco Migliavacca, Marc Garbey Source Type: research
Localization of Optic Disc and Fovea in Retinal Images using Intensity Based Line Scanning Analysis
Accurate detection of diabetic retinopathy (DR) mainly depends on identification of retinal landmarks such as optic disc and fovea. Present methods suffer from challenges like less accuracy and high computational complexity. To address this issue, this paper presents a novel approach for fast and accurate localization of optic disc (OD) and fovea using one-dimensional scanned intensity profile analysis. The proposed method utilizes both time and frequency domain information effectively for localization of OD. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 27, 2017 Category: Bioinformatics Authors: Ravi Kamble, Manesh Kokare, Girish Deshmukh, Fawnizu Azmadi Hussin, Fabrice M ériaudeau Source Type: research
Fuzzy spectral clustering for automated delineation of chronic wound region using digital images
Chronic wound is an abnormal disease condition of localized injury to the skin and its underlying tissues having physiological impaired healing response. Assessment and management of such wound is a significant burden on the healthcare system. Currently, precise wound bed estimation depends on the clinical judgment and remains a difficult task. The paper introduces a novel method for ulcer boundary demarcation and estimation, using optical images captured by a hand-held digital camera. The proposed approach involves gray based fuzzy similarity measure using spatial knowledge of an image. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 22, 2017 Category: Bioinformatics Authors: Dhiraj Manohar Dhane, Maitreya Maiti, Tushar Mungle, Chittaranjan Bar, Arun Achar, Maheshkumar Kolekar, Chandan Chakraborty Source Type: research
Two-phase deep convolutional neural network for reducing class skewness in histopathological images based breast cancer detection
Different types of breast cancer are affecting lives of women across the world. Common types include Ductal carcinoma in situ (DCIS), Invasive ductal carcinoma (IDC), Tubular carcinoma, Medullary carcinoma, and Invasive lobular carcinoma (ILC). While detecting cancer, one important factor is mitotic count – showing how rapidly the cells are dividing. But the class imbalance problem, due to the small number of mitotic nuclei in comparison to the overwhelming number of non-mitotic nuclei, affects the performance of classification models. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 18, 2017 Category: Bioinformatics Authors: Noorul Wahab, Asifullah Khan, Yeon Soo Lee Source Type: research
Automated Detection of Premature Delivery Using Empirical Mode and Wavelet Packet Decomposition Techniques with Uterine Electromyogram Signals
An accurate detection of preterm labor and the risk of preterm delivery before 37 weeks of gestational age is crucial to increase the chance of survival rate for both mother and the infant. Thus, the uterine contractions measured using uterine electromyogram (EMG) or electro hysterogram (EHG) need to have high sensitivity in the detection of true preterm labor signs. However, visual observation and manual interpretation of EHG signals at the time of emergency situation may lead to errors. Therefore, the employment of computer-based approaches can assist in fast and accurate detection during the emergency situation. (Source...
Source: Computers in Biology and Medicine - April 18, 2017 Category: Bioinformatics Authors: U Rajendra Acharya, Vidya K Sudarshan, Soon Qing Rong, Zechariah Tan, Lim Choo Min, Joel EW Koh, Sujatha Nayak, Sulatha V Bhandary Source Type: research
J.S. Athertya, G. Saravana Kumar, “Automatic segmentation of vertebral contours from CT images using fuzzy corners” [Comput. Biol. Med. 72 (May 1, 2016) 75–89, https://www.ncbi.nlm.nih.gov/pubmed/27017068]
To: Dr Edward J. Ciaccio (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: James D. Bilson, Samuel J. Lapworth Source Type: research
Dynamics of a three species ratio-dependent food chain model with intra-specific competition within the top predator
In this paper, a ratio-dependent food chain model has been considered. The total population has been divided into three classes, namely prey, predator and top-predator population. We have also incorporated intra-specific competition of predators in the model. We have studied the boundedness, dissipativeness and permanence of the solutions of the system and analyzed the existence of various equilibrium points and stability of the system at those equilibrium points. The system exhibits Bogdanov-Takens bifurcation, saddle-node bifurcation, Hopf bifurcation for suitable choice of the relevant parameters. (Source: Computers in ...
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: Nijamuddin Ali, Mainul Haque, Ezio Venturino, Santabrata Chakravarty Source Type: research
Automatic cumulative sums contour detection of FBP-reconstructed multi-object nuclear medicine images
The problem of determining the contours of objects in nuclear medicine images has been studied extensively in the past, however most of the analysis has focused on a single object as opposed to multiple objects. The aim of this work is to develop an automated method for determining the contour of multiple objects in positron emission tomography (PET) and single photon emission computed tomography (SPECT) filtered backprojection (FBP) reconstructed images. These contours can be used for computing body edges for attenuation correction in PET and SPECT, as well as for eliminating streak artifacts outside the objects, which co...
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: Nicholas E. Protonotarios, George M. Spyrou, George A. Kastis Source Type: research
Circular Shape Constrained Fuzzy Clustering (CiscFC) for Nucleus Segmentation in Pap Smear Images
Accurate detection and segmentation of cell nucleus is the precursor step towards computer aided analysis of Pap smear images. This is a challenging and complex task due to degree of overlap, inconsistent staining and poor contrast. In this paper, a novel nucleus segmentation method is proposed by incorporating a circular shape function in fuzzy clustering. The proposed method was evaluated quantitatively and qualitatively using the Overlapping Cervical Cytology Image Segmentation Challenge - ISBI 2014 challenge dataset comprised of 945 overlapping Pap smear images. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: Ratna Saha, Mariusz Bajger, Gobert Lee Source Type: research
A novel tool for the identification of correlations in medical data by faceted search
We describe the details of the use case of transplant medicine and the resulting technical architecture of the faceted search application. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: Danilo Schmidt, Oliver Staeck, Klemens Budde, Daniel Sonntag, Hans-J ürgen Profitlich, Matthias Ihle Source Type: research
Athertya JS, Saravana Kumar G. Automatic segmentation of vertebral contours from CT images using fuzzy corners. Comput Biol Med. 2016 May 1;72:75-89. doi:10.1016/j.compbiomed.2016.03.009. Epub 2016 Mar 18. https://www.ncbi.nlm.nih.gov/pubmed/27017068
To: Dr Edward J. Ciaccio (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: James D Bilson, Samuel J Lapworth Source Type: research
Accelerometry-based Assessment and Detection of Early Signs of Balance Deficits
Falls are the cause for more than half of the injury-related hospitalizations among older people. Accurate assessment of individuals ’ fall risk could enable targeted interventions to reduce the risk. This paper presents a novel method for using wearable accelerometers to detect early signs of deficits in balance from gait. Gait acceleration data were analyzed from 35 healthy female participants (73.86 ± 5.40 years). The data were collected with waist-mounted accelerometer and the participants performed three supervised balance tests: Berg Balance Scale (BBS), Timed-Up-and-Go (TUG) and 4 m walk. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - April 14, 2017 Category: Bioinformatics Authors: Heidi Simil ä, Milla Immonen, Miikka Ermes Source Type: research
