Diverse Partner Selection with Brood Recombination in Genetic Programming

The ultimate goal of learning algorithms is to find the best solution from a search space without testing each and every solution available in the search space. During the evolution process new solutions (children) are produced from existing solutions (parents), where new solutions are expected to be better than existing solutions. This paper presents a new parent selection method for the crossover operation in genetic programming. The idea is to promote crossover between two behaviourally (phenotype) diverse parents such that the probability of children being better than their parents increases. The relative phenotype strengths and weaknesses of pairs of parents are exploited to find out if their crossover is beneficial or not (diverse partner selection (DPS)). Based on the probable improvement in children compared to their parents, crossover is either allowed or disallowed. The parents qualifying for crossover through this process are expected to produce much better children and are allowed to produce more children than normal parents through brood recombination (BR). BR helps to explore the search space around diverse parents much more efficiently. Experimental results from different benchmarking problems demonstrate that the proposed method (DPS with BR) improves the performance of genetic programming significantly

A cooperative feature gene extraction algorithm that combines classification and clustering

In feature gene selection, filtering model concerns classification accuracy while ignoring gene redundancy problem. On the other hand, gene clustering finds correlated genes without considering their predictive abilities. It is valuable to enhance their performances by the help of each other. We report a new feature gene extraction algorithm, namely Double-thresholding Extraction of Feature Gene (DEFG), that combines gene filtering and gene clustering. It firstly pre-select feature gene set from the original dataset. A modified gene clustering is then applied to refine this set. In the gene clustering, specific designs are employed to balance the predictive abilities and the redundancies of the extracted feature gene. We have tested DEFG on a microarray dataset and compared its performance with that of two benchmark algorithms. The experimental results show that DEFG is superior to them in terms of internal validation accuracy and external validation accuracy. Also, DEFG can generalize the pattern structure by a small number of training samples. ©2009 IEEE.published_or_final_versio

Kinesin-1 is involved in chondrocytes adhesion to extracellular matrix and motility

Intercalation movement of proliferative chondrocytes is crucial for their columnar organization which is essential for proper function of growth plate cartilage. The conventional motor protein kinesin‐1 directionally transporting various cargos along microtubules might be involved in this polarized cell movement. Kinesin‐1 is suggested to transport unknown cargo(s) modulating focal adhesion (FA) turnover which is a key step in cell movement. To investigate kinesin‐1’s role in chondrocytes intercalation, we generate kinesin‐1 heavy chain (Kif5b) knockout mouse. In the growth plate of KIF5B deficient mouse, we observed abnormal cell morphology and disrupted columnar structure. Isolated mutant chondrocytes show reduced motility and adhesion ability to ECM proteins. Vinculin, the key regulator of focal adhesions, is found as a potential protein associated with KIF5B in mouse chondrocytes. Further study will investigate whether KIF5B affects chondrocytes motility and adhesion via FAs modulation.postprin

Increased expression of cyclooxygenase-2 in first-degree relatives of gastric cancer patients

Aim: To study the expression of cyclooxygenase-2 (COX-2) in human gastric cancer tissues and their paired adjacent mucosa, as well as mucosa from gastric antrum and corpus of the first-degree relatives of the recruited cancer patients. Methods: The expression of COX-2 mRNA in 38 patients with gastric cancer and their 29 first-degree relatives and 18 healthy controls was assessed by the real time RT-PCR. The expression of COX-2 protein was determined by Western blot. Results: A marked increase in COX-2 mRNA expression was found in 20 of 37 (54%) cancerous tissues compared to their respective paired normal mucosa (P<0.001). Interestingly, increased COX-2 mRNA expression was also found in mucosa of the corpus (6/29) and antrum (13/29) of their first-degree relatives. Increased COX-2 mRNA expression was more frequently observed in the antrum biopsies from cancer patients than in the antrum biopsies from healthy controls (P<0.05). In addition, 3 of 23 (13%) patients with atrophic mucosa and 6 of 35 (17%) patients with intestinal metaplasia showed increased COX-2 mRNA expression. Furthermore, COX-2 expression increased in H pylori-positive tissues, especially in antrum mucosa. Conclusion: Increased COX-2 expression is involved in gastric carcinogenesis, and may be necessary for maintenance of the malignant phenotype and contribute to Helicobacter pylori-associated malignant transformation. © 2005 The WJG Press and Elsevier Inc. All rights reserved.published_or_final_versio

Broadband gradient impedance matching using an acoustic metamaterial for ultrasonic transducers

2016-2017 > Academic research: refereed > Publication in refereed journal201804_a bcmaVersion of RecordPublishe

Generation and quality control of lipidomics data for the alzheimers disease neuroimaging initiative cohort.

Alzheimers disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/

Conscious monitoring and control (reinvestment) in surgical performance under pressure.

Research on intraoperative stressors has focused on external factors without considering individual differences in the ability to cope with stress. One individual difference that is implicated in adverse effects of stress on performance is "reinvestment," the propensity for conscious monitoring and control of movements. The aim of this study was to examine the impact of reinvestment on laparoscopic performance under time pressure

Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain

Earlier reports showed that hyperplasia of sympathoadrenal cell precursors during embryogenesis in Nf1-deficient mice is independent of Nf1’s role in down-modulating RAS-MAPK signaling. We demonstrate in zebrafish that nf1 loss leads to aberrant activation of RAS signaling in MYCN-induced neuroblastomas that arise in these precursors, and that the GTPase-activating protein (GAP)-related domain (GRD) is sufficient to suppress the acceleration of neuroblastoma in nf1-deficient fish, but not the hypertrophy of sympathoadrenal cells in nf1 mutant embryos. Thus, even though neuroblastoma is a classical “developmental tumor”, NF1 relies on a very different mechanism to suppress malignant transformation than it does to modulate normal neural crest cell growth. We also show marked synergy in tumor cell killing between MEK inhibitors (trametinib) and retinoids (isotretinoin) in primary nf1a-/- zebrafish neuroblastomas. Thus, our model system has considerable translational potential for investigating new strategies to improve the treatment of very high-risk neuroblastomas with aberrant RAS-MAPK activation

A QM/MM approach for the study of monolayer-protected gold clusters

We report the development and implementation of hybrid methods that combine quantum mechanics (QM) with molecular mechanics (MM) to theoretically characterize thiolated gold clusters. We use, as training systems, structures such as Au25(SCH2-R)18 and Au38(SCH2-R)24, which can be readily compared with recent crystallographic data. We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment. As an example, we demonstrate that calculations of the 1H and 13C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude increase in computational efficiency.Comment: Journal of Materials Science, 201

A Combined Deep Learning-Gradient Boosting Machine Framework for Fluid Intelligence Prediction

The ABCD Neurocognitive Prediction Challenge is a community driven competition asking competitors to develop algorithms to predict fluid intelligence score from T1-w MRIs. In this work, we propose a deep learning combined with gradient boosting machine framework to solve this task. We train a convolutional neural network to compress the high dimensional MRI data and learn meaningful image features by predicting the 123 continuous-valued derived data provided with each MRI. These extracted features are then used to train a gradient boosting machine that predicts the residualized fluid intelligence score. Our approach achieved mean square error (MSE) scores of 18.4374, 68.7868, and 96.1806 for the training, validation, and test set respectively.Comment: Challenge in Adolescent Brain Cognitive Development Neurocognitive Predictio