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https://www.readbyqxmd.com/read/28092810/expectation-and-futurity-the-remarkable-success-of-genetic-determinism
#1
Maurizio Esposito
Genetic determinism is nowadays largely questioned and widely criticized. However, if we look at the history of biology in the last one hundred years, we realize that genetic determinism has always been controversial. Why, then, did it acquire such relevance in the past despite facing longstanding criticism? Through the analysis of some of the ambitious expectations of future scientific applications, this article explores the possibility that part of the historical success of genetic determinism lies in the powerful rhetorical strategies that have connected the germinal matter with alluring bio-technological visions...
January 13, 2017: Studies in History and Philosophy of Biological and Biomedical Sciences
https://www.readbyqxmd.com/read/28092771/plant-peroxisomes-a-nitro-oxidative-cocktail
#2
REVIEW
Francisco J Corpas, Juan B Barroso, José M Palma, Marta Rodriguez-Ruiz
Although peroxisomes are very simple organelles, research on different species has provided us with an understanding of their importance in terms of cell viability. In addition to the significant role played by plant peroxisomes in the metabolism of reactive oxygen species (ROS), data gathered over the last two decades show that these organelles are an endogenous source of nitric oxide (NO) and related molecules called reactive nitrogen species (RNS). Molecules such as NO and H2O2 act as retrograde signals among the different cellular compartments, thus facilitating integral cellular adaptation to physiological and environmental changes...
January 3, 2017: Redox Biology
https://www.readbyqxmd.com/read/28092716/view-points-of-an-ecologist-on-practical-environmental-ethic-socioecology-common-pool-resources-and-conservation
#3
Juan Carlos Castilla
The paper centers on environmental practical ethic point of views according to a professional ecologist. Ecology and the science of Socio-ecology are defined. The framework of the Millennium Ecosystem Assessment initiative (MA 2003), including the use of ecosystems as the environmental unit of analysis, ecosystem services and human well-being as the center for assessment are discussed. Common-pool resources (CPR) and the allegory of the tragedy of the commons are used to illustrate main scientific and ethical environmental approaches, and above all to highlight the case of climate change, considering ″air-atmosphere″ as a CPR...
September 2016: Cuadernos de Bioética: Revista Oficial de la Asociación Española de Bioética y Ética Médica
https://www.readbyqxmd.com/read/28092580/determination-of-the-edge-of-criticality-in-echo-state-networks-through-fisher-information-maximization
#4
Lorenzo Livi, Filippo Maria Bianchi, Cesare Alippi
It is a widely accepted fact that the computational capability of recurrent neural networks (RNNs) is maximized on the so-called "edge of criticality." Once the network operates in this configuration, it performs efficiently on a specific application both in terms of: 1) low prediction error and 2) high short-term memory capacity. Since the behavior of recurrent networks is strongly influenced by the particular input signal driving the dynamics, a universal, application-independent method for determining the edge of criticality is still missing...
January 16, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28092578/experienced-gray-wolf-optimization-through-reinforcement-learning-and-neural-networks
#5
E Emary, Hossam M Zawbaa, Crina Grosan
In this paper, a variant of gray wolf optimization (GWO) that uses reinforcement learning principles combined with neural networks to enhance the performance is proposed. The aim is to overcome, by reinforced learning, the common challenge of setting the right parameters for the algorithm. In GWO, a single parameter is used to control the exploration/exploitation rate, which influences the performance of the algorithm. Rather than using a global way to change this parameter for all the agents, we use reinforcement learning to set it on an individual basis...
January 10, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28092574/dynamics-in-epistasis-analysis
#6
Aseel Awdeh, Hilary Phenix, Mads Kaern, Theodore Perkins
Finding regulatory relationships between genes, including the direction and nature of influence between them, is a fundamental challenge in the field of molecular genetics. One classical approach to this problem is epistasis analysis. Broadly speaking, epistasis analysis infers the regulatory relationships between a pair of genes in a genetic pathway by considering the patterns of change in an observable trait resulting from single and double deletion of genes. While classical epistasis analysis has yielded deep insights on numerous genetic pathways, it is not without limitations...
January 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28092571/machine-learned-replacement-of-n-labels-for-basecalled-sequences-in-dna-barcoding
#7
Eddie Ma, Sujeevan Ratnasingham, Stefan Kremer
This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label...
August 11, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28092569/discovery-of-micrornas-and-transcription-factors-co-regulatory-modules-by-integrating-multiple-types-of-genomic-data
#8
Jiawei Luo, Gen Xiang, Chu Pan
It is well known that regulators known as microRNA (miRNA) and transcription factor (TF) have been found to play an important role in gene regulation. However, there are few researches of collaborative regulatory (co-regulatory) mechanism between miRNA and TF on system level (function level). Meanwhile, recent advances in high-throughput genomic technologies have enabled researchers to collect diverse large-scale genomic data, which can be used to study the co-regulatory mechanism between miRNA and TF. In this paper, we propose a novel method called SNCoNMF (Sparse Network regularized non-negative matrix factorization for Co-regulatory modules identification) which adopts multiple non-negative matrix factorization framework to identify co-regulatory modules including miRNAs, TFs and genes...
January 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092568/equivalent-discrete-time-channel-modeling-for-molecular-communication-with-emphasize-on-an-absorbing-receiver
#9
Martin Damrath, Sebastian Korte, Peter Hoeher
This paper introduces the equivalent discrete-time channel model (EDTCM) to the area of diffusion-based molecular communication (DBMC). Emphasize is on an absorbing receiver, which is based on the so-called first passage time concept. In the wireless communications community the EDTCM is well known. Therefore, it is anticipated that the EDTCM improves the accessibility of DBMC and supports the adaptation of classical wireless communication algorithms to the area of DBMC. Furthermore, the EDTCM has the capability to provide a remarkable reduction of computational complexity compared to random walk based DBMC simulators...
January 10, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092557/single-image-super-resolution-using-global-regression-based-on-multiple-local-linear-mappings
#10
Jae-Seok Choi, Munchurl Kim
Super-resolution (SR) has become more vital, because of its capability to generate high-quality ultra-high definition (UHD) high-resolution (HR) images from low-resolution (LR) input images. Conventional SR methods entail high computational complexity, which makes them difficult to be implemented for up-scaling of full-high-definition (FHD) input images into UHD-resolution images. Nevertheless, our previous super-interpolation (SI) method showed a good compromise between PSNR performances and computational complexity...
January 10, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092550/-l_0-gradient-projection
#11
Shunsuke Ono
Minimizing L0 gradient, the number of the nonzero gradients of an image, together with a quadratic datafidelity to an input image has been recognized as a powerful edge-preserving filtering method. However, the L0 gradient minimization has an inherent difficulty: a user-given parameter controlling the degree of flatness does not have a physical meaning since the parameter just balances the relative importance of the L0 gradient term to the quadratic data-fidelity term. As a result, the setting of the parameter is a troublesome work in the L0 gradient minimization...
January 11, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092549/learning-short-binary-codes-for-large-scale-image-retrieval
#12
Li Liu, Mengyang Yu, Ling Shao
Large-scale visual information retrieval has become an active research area in this big data era. Recently, hashing/ binary coding algorithms prove to be effective for scalable retrieval applications. Most existing hashing methods require relatively long binary codes (i.e., over hundreds of bits, sometimes even thousands of bits) to achieve reasonable retrieval accuracies. However, for some realistic and unique applications such as on wearable or mobile devices, only short binary codes can be used for efficient image retrieval due to the limitation of computational resources or bandwidth on these devices...
January 11, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092545/heterogeneous-face-recognition-a-common-encoding-feature-discriminant-approach
#13
Dihong Gong, Zhifeng Li, Weilin Huang, Xuelong Li, Dacheng Tao
Heterogeneous face recognition is an important yet challenging problem in face recognition community. It refers to matching a probe face image to a gallery of face images taken from alternate imaging modality. The major challenge of heterogeneous face recognition lies in the great discrepancies between different image modalities. Conventional face feature descriptors, e.g. LBP, HOG and SIFT, are mostly designed in a handcrafted way and thus generally fail to extract the common discriminant information from the heterogeneous face images...
January 10, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092535/super-resolution-person-re-identification-with-semi-coupled-low-rank-discriminant-dictionary-learning
#14
Xiao-Yuan Jing, Xiaoke Zhu, Fei Wu, Ruimin Hu, Xinge You, Yunhong Wang, Hui Feng, Jing-Yu Yang
Person re-identification has been widely studied due to its importance in surveillance and forensics applications. In practice, gallery images are high-resolution (HR) while probe images are usually low-resolution (LR) in the identification scenarios with large variation of illumination, weather or quality of cameras. Person re-identification in this kind of scenarios, which we call super-resolution (SR) person re-identification, has not been well studied. In this paper, we propose a semi-coupled low-rank discriminant dictionary learning (SLD2L) approach for SR person re-identification task...
January 10, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092506/wideband-2-d-array-design-optimization-with-fabrication-constraints-for-3-d-us-imaging
#15
Emmanuel Roux, Alessandro Ramalli, Herve Liebgott, Christian Cachard, Marc C Robini, Piero Tortoli
Ultrasound (US) 2-D arrays are of increasing interest due to their electronic steering capability to investigate 3-D regions without requiring any probe movement. These arrays are typically populated by thousands of elements that, ideally, should be individually driven by the companion scanner. Since this is not convenient, the so-called microbeamforming methods, yielding a prebeamforming stage performed in the probe handle by suitable custom integrated circuits, have so far been implemented in a few commercial high-end scanners...
January 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#16
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28092441/local-mode-analysis-decoding-ir-spectra-by-visualizing-molecular-details
#17
Matthias Massarczyk, Till Rudack, Jürgen Schlitter, Jens Kuhne, Carsten Kötting, Klaus Gerwert
Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call Local Mode Analysis (LMA) for calculating IR spectra and assigning spectral IR bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory...
January 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28092408/network-structure-and-local-adaptation-in-coevolving-bacteria-phage-interactions
#18
James Gurney, Lafi Aldakak, Alex Betts, Claire Gougat-Barbera, Timothée Poisot, Oliver Kaltz, Michael E Hochberg
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so called 'bipartite networks', reflected observed coevolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts...
January 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28092254/-what-do-adults-die-in-mexico-impact-on-the-economic-and-social-development-of-the-nation-the-global-burden-of-cardiovascular-disease
#19
Martín Rosas-Peralta, Efraín Arizmendi-Uribe, Gabriela Borrayo-Sánchez
Noncommunicable diseases have been established as a clear threat, not only to human health but also to the development and economic growth. Claiming 63% of all deaths, these diseases are currently the main murderer worldwide. The increase in the prevalence and importance of noncommunicable diseases specifically of cardiovascular risk factors such as hypertension, diabetes, dyslipidemia and obesity is the result of a complex interplay between health, economic growth and development, which is strongly associated with universal trends such as the aging of the world population, rapid unplanned urbanization, and the globalization of unhealthy lifestyles...
January 2017: Revista Médica del Instituto Mexicano del Seguro Social
https://www.readbyqxmd.com/read/28091933/flagellar-regulation-and-virulence-in-the-entomopathogenic-bacteria-xenorhabdus-nematophila-and-photorhabdus-luminescens
#20
Alain Givaudan, Anne Lanois
There is a complex interplay between the regulation of flagellar motility and the expression of virulence factors in many bacterial pathogens. Here, we review the literature on the direct and indirect roles of flagellar motility in mediating the tripartite interaction between entomopathogenic bacteria (Photorhabdus and Xenorhabdus), their nematode hosts, and their insect targets. First, we describe the swimming and swarming motility of insect pathogenic bacteria and its impact on insect colonization. Then, we describe the coupling between the expression of flagellar and virulence genes and the dynamic of expression of the flagellar regulon during invertebrate infection...
December 28, 2016: Current Topics in Microbiology and Immunology
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