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https://www.readbyqxmd.com/read/29244011/a-deep-learning-method-for-lincrna-detection-using-auto-encoder-algorithm
#1
Ning Yu, Zeng Yu, Yi Pan
BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29240533/investigation-of-perceptual-motor-behavior-across-the-expert-athlete-to-disabled-patient-skill-continuum-can-advance-theory-and-practical-application
#2
Sean Müller, Ann-Maree Vallence, Carolee Winstein
A framework is presented of how theoretical predictions can be tested across the expert athlete to disabled patient skill continuum. Common-coding theory is used as the exemplar to discuss sensory and motor system contributions to perceptual-motor behavior. Behavioral and neural studies investigating expert athletes and patients recovering from cerebral stroke are reviewed. They provide evidence of bi-directional contributions of visual and motor systems to perceptual-motor behavior. Majority of this research is focused on perceptual-motor performance or learning, with less on transfer...
December 14, 2017: Journal of Motor Behavior
https://www.readbyqxmd.com/read/29238299/the-htm-spatial-pooler-a-neocortical-algorithm-for-online-sparse-distributed-coding
#3
Yuwei Cui, Subutai Ahmad, Jeff Hawkins
Hierarchical temporal memory (HTM) provides a theoretical framework that models several key computational principles of the neocortex. In this paper, we analyze an important component of HTM, the HTM spatial pooler (SP). The SP models how neurons learn feedforward connections and form efficient representations of the input. It converts arbitrary binary input patterns into sparse distributed representations (SDRs) using a combination of competitive Hebbian learning rules and homeostatic excitability control...
2017: Frontiers in Computational Neuroscience
https://www.readbyqxmd.com/read/29237855/sex-specific-adaptation-and-genomic-responses-to-y-chromosome-presence-in-female-reproductive-and-neural-tissues
#4
Alan T Branco, Rute M Brito, Bernardo Lemos
Y chromosomes typically harbour a small number of genes and an abundance of repetitive sequences. In Drosophila, the Y chromosome comprises multimegabase long segments of repetitive DNA and a handful of protein-coding genes. In mammals, the Y chromosome also harbours a disproportionally high abundance of repeats. Here, we built on a Drosophila melanogaster model in which the Y chromosome is decoupled from sexual determination. Genotypes were genetically identical for the autosomes, X chromosome, and mitochondria, but differ by the presence or dose of the Y chromosome...
December 20, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29236787/efficient-enhancement-of-information-in-the-prefrontal-cortex-during-the-presence-of-reward-predicting-stimuli
#5
Camilo J Mininni, César F Caiafa, B Silvano Zanutto, Kuei Y Tseng, Sergio E Lew
The prefrontal cortex (PFC) is a key brain structure for decision making, behavioural flexibility and working memory. Neurons in PFC encode relevant stimuli through changes in their firing rate, although the metabolic cost of spiking activity puts strong constrains to neural codes based on firing rate modulation. Thus, how PFC neural populations code relevant information in an efficient way is not clearly understood. To address this issue we made single unit recordings in the PFC of rats performing a GO/NOGO discrimination task and analysed how entropy between pairs of neurons changes during cue presentation...
2017: PloS One
https://www.readbyqxmd.com/read/29236718/particle-swarm-optimization-based-automatic-parameter-selection-for-deep-neural-networks-and-its-applications-in-large-scale-and-high-dimensional-data
#6
Fei Ye
In this paper, we propose a new automatic hyperparameter selection approach for determining the optimal network configuration (network structure and hyperparameters) for deep neural networks using particle swarm optimization (PSO) in combination with a steepest gradient descent algorithm. In the proposed approach, network configurations were coded as a set of real-number m-dimensional vectors as the individuals of the PSO algorithm in the search procedure. During the search procedure, the PSO algorithm is employed to search for optimal network configurations via the particles moving in a finite search space, and the steepest gradient descent algorithm is used to train the DNN classifier with a few training epochs (to find a local optimal solution) during the population evaluation of PSO...
2017: PloS One
https://www.readbyqxmd.com/read/29234861/neural-coding-of-sound-envelope-structure-in-songbirds
#7
Santiago Boari, Ana Amador
Songbirds are a well-established animal model to study the neural basis of learning, perception and production of complex vocalizations. In this system, telencephalic neurons in HVC present a state-dependent, highly selective response to auditory presentations of the bird's own song (BOS). This property provides an opportunity to study the neural code behind a complex motor behavior. In this work, we explore whether changes in the temporal structure of the sound envelope can drive changes in the neural responses of highly selective HVC units...
December 12, 2017: Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology
https://www.readbyqxmd.com/read/29232014/mutations-of-the-glycine-cleavage-system-genes-possibly-affect-the-negative-symptoms-of-schizophrenia-through-metabolomic-profile-changes
#8
Akane Yoshikawa, Fumichika Nishimura, Aya Inai, Yosuke Eriguchi, Masaki Nishioka, Atsuhiko Takaya, Mamoru Tochigi, Yoshiya Kawamura, Tadashi Umekage, Kayoko Kato, Tsukasa Sasaki, Yoshiaki Ohashi, Kazuya Iwamoto, Kiyoto Kasai, Chihiro Kakiuchi
AIM: Hypofunction of N-methyl-D-aspartate receptors (NMDARs) may contribute to the pathophysiology of schizophrenia (SCZ). Recently, the glycine cleavage system (GCS) was shown to affect NMDAR function in the brain. GCS functional defects cause nonketotic hyperglycinemia (NKH), the atypical phenotype of which presents psychiatric symptoms similar to SCZ. Here, we examined the involvement of GCS in SCZ. METHODS: First, to identify the rare variants and the exonic deletions, we re-sequenced all the coding exons and the splice sites of four GCS genes (GLDC, AMT, GCSH, DLD) in 474 patients with SCZ and 475 controls and performed multiplex ligation-dependent probe amplification (MLPA) analysis in SCZ...
December 12, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29231074/hybrid-response-surface-methodology-artificial-neural-network-optimization-of-drying-process-of-banana-slices-in-a-forced-convective-dryer
#9
Amin Taheri-Garavand, Fatemeh Karimi, Mahmoud Karimi, Valiullah Lotfi, Golmohammad Khoobbakht
The aim of the study is to fit models for predicting surfaces using the response surface methodology and the artificial neural network to optimize for obtaining the maximum acceptability using desirability functions methodology in a hot air drying process of banana slices. The drying air temperature, air velocity, and drying time were chosen as independent factors and moisture content, drying rate, energy efficiency, and exergy efficiency were dependent variables or responses in the mentioned drying process...
January 1, 2017: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/29229773/ap-2%C3%AE-and-ap-2%C3%AE-cooperatively-orchestrate-homeobox-gene-expression-during-branchial-arch-patterning
#10
Eric Van Otterloo, Hong Li, Kenneth L Jones, Trevor Williams
The evolution of a hinged moveable jaw with variable morphology is considered a major factor behind the successful expansion of the vertebrates. DLX homeobox transcription factors are critical to establish the positional code that patterns the mandible, maxilla and intervening hinge domain, but how these genes are regulated remains unclear. Herein, we demonstrate that the concerted action of the AP-2ɑ and AP-2β transcription factors within the mouse neural crest is essential for jaw patterning. In the absence of these two genes the hinge domain is lost and there are alterations in the size and patterning of the jaws correlating with dysregulation of homeobox gene expression, with reduced levels of Emx, Msx and Dlx paralogs accompanied by an expansion of Six1...
December 11, 2017: Development
https://www.readbyqxmd.com/read/29228185/dncon2-improved-protein-contact-prediction-using-two-level-deep-convolutional-neural-networks
#11
Badri Adhikari, Jie Hou, Jianlin Cheng
Motivation: Significant improvements in the prediction of protein residue-residue contacts are observed in the recent years. These contacts, predicted using a variety of coevolution-based and machine learning methods, are the key contributors to the recent progress in ab initio protein structure prediction, as demonstrated in the recent CASP experiments. Continuing the development of new methods to reliably predict contact maps is essential to further improve ab initio structure prediction...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29228141/the-source-of-visual-size-adaptation
#12
Hang Zeng, Sylvia Kreutzer, Gereon R Fink, Ralph Weidner
Size adaptation describes the tendency of the visual system to adjust neural responsiveness of size representations after prolonged exposure to particular stimulations. A larger (or smaller) adaptor stimulus influences the perceived size of a similar test stimulus shown subsequently. Size adaptation may emerge on various processing levels. Functional representations of the adaptor to which the upcoming stimulus is adapted may be coded early in the visual system mainly reflecting retinal size. Alternatively, size adaptation may involve higher order processes that take into account additional information such as an object's estimated distance from the observer, hence reflecting perceived size...
December 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/29222906/low-maternal-folate-concentrations-and-maternal-mthfr-c677t-polymorphism-are-associated-with-an-increased-risk-for-neural-tube-defects-in-offspring-a-case-control-study-among-pakistani-case-and-control-mothers
#13
Nuzhat Nauman, Samina Jalali, Sajjad Shami, Shireen Rafiq, Greta Große, Alina C Hilger, Rhong Zhang, Saira Mansoor, Michael Ludwig, Heiko Reutter
BACKGROUND AND OBJECTIVES: There is considerable evidence that periconceptional maternal folate deficiency and coding variants in maternal genes coding for critical enzymes in the folate pathway are associated with neural tube defects (NTDs) in offspring. In a case-control study we investigated C677T polymorphism in the 5,10- methylenetetrahydrofolate reductase (MTHFR) gene in case and control mothers of Pakistani origin, and compared these with the respective maternal folate concentrations measured at the time of delivery...
2018: Asia Pacific Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/29222729/coding-of-time-dependent-stimuli-in-homogeneous-and-heterogeneous-neural-populations
#14
Manuel Beiran, Alexandra Kruscha, Jan Benda, Benjamin Lindner
We compare the information transmission of a time-dependent signal by two types of uncoupled neuron populations that differ in their sources of variability: i) a homogeneous population whose units receive independent noise and ii) a deterministic heterogeneous population, where each unit exhibits a different baseline firing rate ('disorder'). Our criterion for making both sources of variability quantitatively comparable is that the interspike-interval distributions are identical for both systems. Numerical simulations using leaky integrate-and-fire neurons unveil that a non-zero amount of both noise or disorder maximizes the encoding efficiency of the homogeneous and heterogeneous system, respectively, as a particular case of suprathreshold stochastic resonance...
December 8, 2017: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29222469/hippocampal-oxytocin-receptors-are-necessary-for-discrimination-of-social-stimuli
#15
Tara Raam, Kathleen M McAvoy, Antoine Besnard, Alexa Veenema, Amar Sahay
Oxytocin receptor (Oxtr) signaling in neural circuits mediating discrimination of social stimuli and affiliation or avoidance behavior is thought to guide social recognition. Remarkably, the physiological functions of Oxtrs in the hippocampus are not known. Here we demonstrate using genetic and pharmacological approaches that Oxtrs in the anterior dentate gyrus (aDG) and anterior CA2/CA3 (aCA2/CA3) of mice are necessary for discrimination of social, but not non-social, stimuli. Further, Oxtrs in aCA2/CA3 neurons recruit a population-based coding mechanism to mediate social stimuli discrimination...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29220307/from-winner-takes-all-to-winners-share-all-exploiting-the-information-capacity-in-temporal-codes
#16
Melika Payvand, Luke Theogarajan
In this letter, we have implemented and compared two neural coding algorithms in the networks of spiking neurons: Winner-takes-all (WTA) and winners-share-all (WSA). Winners-Share-All exploits the code space provided by the temporal code by training a different combination of [Formula: see text] out of [Formula: see text] neurons to fire together in response to different patterns, while WTA uses a one-hot-coding to respond to distinguished patterns. Using WSA, the maximum value of [Formula: see text] in order to maximize information capacity using [Formula: see text] output neurons was theoretically determined and utilized...
December 8, 2017: Neural Computation
https://www.readbyqxmd.com/read/29218893/discriminative-bag-of-cells-for-imaging-genomics
#17
Benjamin Chidester, Minh N Do, Jian Ma
Connecting genotypes to image phenotypes is crucial for a comprehensive understanding of cancer. To learn such connections, new machine learning approaches must be developed for the better integration of imaging and genomic data. Here we propose a novel approach called Discriminative Bag-of-Cells (DBC) for predicting genomic markers using imaging features, which addresses the challenge of summarizing histopathological images by representing cells with learned discriminative types, or codewords. We also developed a reliable and efficient patch-based nuclear segmentation scheme using convolutional neural networks from which nuclear and cellular features are extracted...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218861/comparative-expression-patterns-of-sox2-and-sox19-genes-in-the-forebrain-of-developing-and-adult-turbot-scophthalmus-maximus
#18
Xoana Taboada, Ana Viñas, Fátima Adrio
The turbot, Scophthalmus maximus, belongs to the flatfishes (order Pleuronectiformes), which display substantial asymmetry of the olfactory organs and forebrain. Sox genes code for SRY-related HMG domain-bearing transcription factors involved in various developmental processes. Group B1 Sox genes as Sox2 and Sox19 appear to play major roles in neural development. Here, we characterized by in situ hybridization the developmental expression of Sox2 and Sox19 genes in metamorphic and postmetamorphic specimens and young adults of both sexes...
December 8, 2017: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/29214513/hyper-response-to-novelty-increases-c-fos-expression-in-the-hippocampus-and-prefrontal-cortex-in-a-rat-model-of-schizophrenia
#19
Tomas Monfil, Rubén Antonio Vázquez Roque, Israel Camacho-Abrego, Hiram Tendilla-Beltran, Tommaso Ianniti, Ivan Meneses-Morales, Patricia Aguilar-Alonso, Gonzalo Flores, Julio Cesar Morales-Medina
Schizophrenia is a debilitating disorder that may have a neurodevelopmental origin. For this reason, animal models based on neonatal insults or manipulations have been extensively used to demonstrate schizophrenia-related behaviors. Among those, the neonatal ventral hippocampus lesion (nVHL) is largely used as a model of schizophrenia-related behavior as it mimics behavioral and neurochemical abnormalities often seen in schizophrenic patients including hyperlocomotion in a novel environment. To investigate the neuroanatomical basis of coding novelty in the nVHL rat, we assessed the behavioral locomotor activity paradigm in a novel environment and measured expression of c-Fos, a marker of neural activation, in brain regions involved in the process of coding novelty or locomotion...
December 6, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/29214085/sox5-null-heterozygous-mutation-in-a-family-with-adult-onset-hyperkinesia-and-behavioral-abnormalities
#20
Michael Zech, Katharina Poustka, Sylvia Boesch, Riccardo Berutti, Tim M Strom, Wolfgang Grisold, Werner Poewe, Juliane Winkelmann
SOX5 encodes a conserved transcription factor implicated in cell-fate decisions of the neural lineage. SOX5 haploinsufficiency induced by larger genomic deletions has been linked to a recognizable pediatric syndrome combining developmental delay with intellectual disability, mild dysmorphism, inadequate behavior, and variable additional features including motor disturbances. In contrast to SOX5-involving deletions, examples of pathogenic SOX5 small coding variations are sparse in the literature and have been described only in singular cases with phenotypic abnormalities akin to those seen in the SOX5 microdeletion syndrome...
2017: Case Reports in Genetics
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