Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining Associations Between Genetic Markers, Phenotypes, and Covariates

We used Haplotype Pattern Mining, HPM [Toivonen et al., Am J Hum Genet 67:133–45, 2000], for gene localization in Genetic Analysis Workshop (GAW) 12 isolate data. In HPM, association is analyzed by searching all trait‐associated haplotype patterns. Data mining algorithms are utilized to make the search efficient. The strength of the haplotype‐trait associations is measured by a linear model, into which a pre‐selected set of covariates is incorporated. Marker‐wise patterns of association are used for predicting the disease gene location. Genome‐wide scans of susceptibility genes for affection status as well as for the quantitative traits (Q1–Q5) were performed. First analyses were made with small sample sizes, 63–94 trios per trait, which is compared with a pilot study of a larger complex disease‐mapping project. Subsequently, the analysis was repeated with approximately 600 cases and 600 controls per trait to give higher power to the analyses. With small sample sizes, only the susceptibility genes having the strongest effects on the traits could be localized. The larger sample size gave very good results: all susceptibility genes, except one, could be correctly localized. First experiments on candidate genes suggested that HPM is applicable even to fine mapping of mutations in DNA sequence. © 2001 Wiley‐Liss, Inc.
The Advantage of Ambiguity? Enhanced Neural Responses to Multi-Stable Percepts Correlate with the Degree of Perceived Instability

Artwork can often pique the interest of the viewer or listener as a result of the ambiguity or instability contained within it. Our engagement with uncertain sensory experiences might have its origins in early cortical responses, in that perceptually unstable stimuli might preclude neural habituation and maintain activity in early sensory areas. To assess this idea, participants engaged with an ambiguous visual stimulus wherein two squares alternated with one another, in terms of simultaneously opposing vertical and horizontal locations relative to fixation (i.e., stroboscopic alternating motion; von Schiller, 1933). At each trial, participants were invited to interpret the movement of the squares in one of five ways: traditional vertical or horizontal motion, novel clockwise or counter-clockwise motion, and, a free-view condition in which participants were encouraged to switch the direction of motion as often as possible. Behavioral reports of perceptual stability showed clockwise and counter-clockwise motion to possess an intermediate level of stability compared to relatively stable vertical and horizontal motion, and, relatively unstable motion perceived during free-view conditions. Early visual evoked components recorded at parietal–occipital sites such as C1, P1, and N1 modulated as a function of visual intention. Both at a group and individual level, increased perceptual instability was related to increased negativity in all three of these early visual neural responses. Engagement with increasingly ambiguous input may partly result from the underlying exaggerated neural response to it. The study underscores the utility of combining neuroelectric recording with the presentation of perceptually multi-stable yet physically identical stimuli, in revealing brain activity associated with the purely internal process of interpreting and appreciating the sensory world that surrounds us.
Development and experimentation of TCP initial window function

In the light of the mice-elephant phenomenon of the Internet traffic, TCP congestion control algorithm shows unfairness against flows of small sizes (small flows). In this context, we find it motivating to study the influence of TCP's initial window (IW) size on the response times of small flows. In our previous works, we proposed a function that determines IW-size for each flow based on its size; through game-theoretic analysis as well as experiments on real testbed, we observed that the size-based IW function (in comparison to a single constant IW size) shows considerable improvement in the performance of small flows, while at the same time not affecting the performance of large flows. In this paper, we share the experience of using some important open source tools for developing, experimenting and evaluating the proposed IW function. We implement the size-based IW function in the Linux kernel, version 3.7. 4; we use ipfw/Dummynet for emulating links, open source tool called parallel for executing the application in parallel for generating TCP traffic, wireshark (along with lua script) for extracting metrics for performance analysis. Finally we evaluate the performance of flows using the IW function.
XNeuroGene: a system for evolving artificial neural networks

Artificial nervous systems (ANS) controlling action coordination tasks are in general very difficult to design. This is partly due to the great number of parameters that can be optimized: neural net connectivity, neuron functionality, weight settings etc. Another problem is posed by the need to automatically construct neuron clusters (modules) which can subsequently be used as building blocks. We focus on the description of a graphical user interface and management system (XNeuroGene) for NeuroGene which automatically assembles and optimizes artificial nervous systems based on evolutionary/genetic programming methods. <<ETX>>
Revised STandards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA): extending the CONSORT statement

The STandards for Reporting Interventions in Clinical Trials of Acupuncture (STRICTA) were published in five journals in 2001 and 2002. These guidelines, in the form of a checklist and explanations for use by authors and journal editors, were designed to improve reporting of acupuncture trials, particularly the interventions, thereby facilitating their interpretation and replication. Subsequent reviews of the application and impact of STRICTA have highlighted the value of STRICTA as well as scope for improvements and revision. To manage the revision process a collaboration between the STRICTA Group, the CONSORT Group and the Chinese Cochrane Centre was developed in 2008. An expert panel with 47 participants was convened that provided electronic feedback on a revised draft of the checklist. At a subsequent face-to-face meeting in Freiburg, a group of 21 participants further revised the STRICTA checklist and planned dissemination. The new STRICTA checklist, which is an official extension of CONSORT, includes 6 items and 17 subitems. These set out reporting guidelines for the acupuncture rationale, the details of needling, the treatment regimen, other components of treatment, the practitioner background and the control or comparator interventions. In addition, and as part of this revision process, the explanations for each item have been elaborated, and examples of good reporting for each item are provided. In addition, the word ‘controlled’ in STRICTA is replaced by ‘clinical’, to indicate that STRICTA is applicable to a broad range of clinical evaluation designs, including uncontrolled outcome studies and case reports. It is intended that the revised STRICTA checklist, in conjunction with both the main CONSORT statement and extension for non-pharmacological treatment, will raise the quality of reporting of clinical trials of acupuncture.
Automatic annotation of histopathological images using a latent topic model based on non-negative matrix factorization

Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively.
Human Neuroscience

prefrontal cortex. Studies of resting-state functional connectivity MRI (rs-fcMRI), confi rmed the segregation of the regions into two networks (Fair et al., 2007; Dosenbach et al., 2008). The combined results from the functional MRI (fMRI) meta-analysis and the subsequent rs-fcMRI analyses (suggest that there are brain regions consistently involved in separable aspects of top-down control over a variety of tasks. One network of regions has positive sustained activity across the duration of a task, suggesting its involvement as a " task-maintenance " network. The other network contains regions showing primarily task initiation signal, suggesting that it may act as a faster, adaptive control network. In principle, should abnormal processing occur at either of these timescales, the result could be unintentional and/or undesired behaviors.
Genetics of addictions: strategies for addressing heterogeneity and polygenicity of substance use disorders

Addictions are common psychiatric disorders that exert high cost to the individual and to society. Addictions are a result of the interplay of multiple genetic and environmental factors. They are characterized by phenotypic and genetic heterogeneity as well as polygenicity, implying a contribution of different neurobiological mechanisms to the clinical diagnosis. Therefore, treatments for most substance use disorders are often only partially effective, with a substantial proportion of patients failing to respond. To address heterogeneity and polygenicity, strategies have been developed to identify more homogeneous subgroups of patients and to characterize genes contributing to their phenotype. These include genetic linkage and association studies as well as functional genetic analysis using endophenotypes and animal behavioural experimentation. Applying these strategies in a translational context aims at improving therapeutic response by the identification of subgroups of addiction patients for individualized, targeted treatment strategies. This article aims to discuss strategies addressing heterogeneity and polygenicity of substance use disorders by presenting results of recent research on genetic and environmental components of addiction. It will also introduce the European IMAGEN study that aims to integrate methodical approaches discussed in order to identify the genetic and neurobiological basis of behavioural traits relevant to the development of addictions.
Molecular characterization of banana NAC transcription fac ors and their interac ions with ethylene signalling component EIL during fruit ripening

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short(6 h) and long(2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.
solation and chara terization of GtMYBP 3 d GtMYBP 4 , orthologues of R 2 R 3-MYB transcription factors that regulate early flavonoid biosynthesis , in gentian flowers

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short(6 h) and long(2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.
creased leaf photosynthesis caused by elevat d stomatal conductance in a rice mutant d fic ent in SLAC 1 , a guard cell anion channel protein

In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short(6 h) and long(2 d or 4 d) term and low (10 mM) and high (50 mM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.
Distance-Based Encryption: How to Embed Fuzziness in Biometric-Based Encryption

We introduce a new encryption notion called distance-based encryption (DBE) to apply biometrics in identity-based encryption. In this notion, a ciphertext encrypted with a vector and a threshold value can be decrypted with a private key of another vector, if and only if the distance between these two vectors is less than or equal to the threshold value. The adopted distance measurement is called Mahalanobis distance, which is a generalization of Euclidean distance. This novel distance is a useful recognition approach in the pattern recognition and image processing community. The primary application of this new encryption notion is to incorporate biometric identities, such as face, as the public identity in an identity-based encryption. In such an application, usually the input biometric identity associated with a private key will not be exactly the same as the input biometric identity in the encryption phase, even though they are from the same user. The introduced DBE addresses this problem well as the decryption condition does not require identities to be identical but having small distance. The closest encryption notion to DBE is the fuzzy identity-based encryption, but it measures biometric identities using a different distance called an overlap distance (a variant of Hamming distance) that is not widely accepted by the pattern recognition community, due to its long binary representations. In this paper, we study this new encryption notion and its constructions. We show how to generically and efficiently construct such a DBE from an inner product encryption (IPE) with reasonable size of private keys and ciphertexts. We also propose a new IPE scheme with the shortest private key to build DBE, namely, the need for a short private key. Finally, we study the encryption efficiency of DBE by splitting our IPE encryption algorithm into offline and online algorithms.
Fabrication and dielectric properties of highly loaded polypropylene micro- and nano-composites

Composites of polypropylene (PP) containing between 50 and 80 wt% of hexagonal Boron Nitride (hBN) were prepared by planetary milling. The additive was both nanometric and micrometric. Samples containing a mix of half nanoparticles and half microparticles were also fabricated in order to test the possible allying of micro and nanocomposites properties. Highly loaded PP showed much higher dielectric losses, especially when filled with micrometric hBN, and consequently a higher dielectric constant. The breakdown strength was maintained at similar values than the neat polymer up to 70 wt% and then was found to decrease significantly. The thermal conductivity was only noticeably higher than the one of neat PP but did not seem to be strongly affected by a variation of concentration from 50 to 80 %. Thermo Gravimetric Analysis was conducted to study the possible contamination during fabrication.
A Hybrid Approach to Biomedical Named Entity Recognition and Semantic Role Labeling

In this paper, we describe our hybrid approach to two key NLP technologies: biomedical named entity recognition (Bio-NER) and (Bio-SRL). In Bio-NER, our system successfully integrates linguistic features into the CRF framework. In addition, we employ web lexicons and template-based post-processing to further boost its performance. Through these broad linguistic features and the nature of CRF, our system outperforms state-of-the-art machine-learning-based systems, especially in the recognition of protein names (F=78.5%). In Bio-SRL, first, we construct a proposition bank on top of the popular biomedical GENIA treebank following the PropBank annotation scheme. We only annotate the predicate-argument structures (PAS's) of thirty frequently used biomedical verbs (predicates) and their corresponding arguments. Second, we use our proposition bank to train a biomedical SRL system, which uses a maximum entropy (ME) machine-learning model. Thirdly, we automatically generate argument-type templates, which can be used to improve classification of biomedical argument roles. Our experimental results show that a newswire English SRL system that achieves an F-score of 86.29% in the newswire English domain can maintain an F-score of 64.64% when ported to the biomedical domain. By using our annotated biomedical corpus, we can increase that F-score by 22.9%. Adding automatically generated template features further increases overall F-score by 0.47% and adjunct (AM) F-score by 1.57%, respectively.
Realistic occlusion effects in mirror-based co-located augmented reality systems

This paper describes the incorporation of realistic occlusion effects into mirror-based, stereoscopic co-location augmented reality display systems. By adding a light-blocking device in the form of an LCD panel underneath the semi-transparent mirror, the view on the physical world can be selectively blocked out such that virtual objects can fully occlude physical objects. Furthermore, by removing areas of the virtual objects rendered on the reflected display, physical objects seen through the semi-transparent mirror and the transmissive LCD panel appear to occlude these virtual objects. We describe the governing principles of the approach, and present an efficient algorithm for the generation of the occlusion masks with the use of vision-based scene reconstruction. Finally, a first prototype implementation of the system is presented.
Species Diversity of Macrophytes of the New Calabar River, Niger Delta, Nigeria

Survey of macrophytes from the New Calabar River was conducted to quantify the species diversity. The macrophytes studies were conducted between December and May 2014 along the edge and in the middle of the River. Ten families of macrophyte were recorded representing 12 species. Cyperaceae had the highest species with three species while the remaining had one specie each. The result of this study showed that Rhynchospora corymbosa had the highest abundance (richness), followed by C.difformis while the species lowest abundance (richness) was Eichhornia crassipes, Nymphaea lotus was the lowest in evenness (distribution) followed by Aneilema beniniense and Platostoma africana having the same level of distribution. Aspilia africana had the highest evenness. The diversity indices indicated that Rhynchospora corymbosa had the highest taxa value 65, Shannon Weinner 4.01, Simpsons 0.98 and Margalef 7.60 while Eichhornia crassipes recorded the lowest taxa of 17, Shannon Weinner had 2.72, Simpsons 0.92 and Margalef 2.30 respectively for macrophytes. The biotic indices of Margalef’s species richness, Shannon - Wiener information function, evenness and Simpson’s Dominance were fairly distributed in the River. This showed that the macrophytes in the study area were stable.
An approach that will NoC your SoCs off!

New structured communication fabrics, called networks on chips (NoCs), have emerged for use in SoC designs. The basic concept is to communicate across the chip in the same way that messages are transmitted over the internet today. That is, put a packet-switching network on the chip and send messages back and forth between blocks. Designers have already resolved most of the issues in the Internet domain, so it's just a matter of bringing that knowledge to the chip. Of course, NoC is not a panacea. It does seem appropriate for the multiprocessor SoC platforms that are homogeneous in nature, but the jury is still out on the value of NoC for chips with heterogeneous IP blocks.
Automated Early Cancer Screening Based on Kernel Method

An automated method that detects early cancerous specimens based on image analysis is described. After acquisition and noise reduction, the microscope images are segmented into individual cell nucleus, from which the feature vectors of nucleus are calculated. The dimensionality of the feature vectors is then reduced using a method combing F-Score and random forest algorithms. The types of the cell nucleus are identified by a classifier based on a non-linear kernel method, and the diagnosis is made on the basis of the statistics. The method was experimented on a data set of 25,000 cell nucleus instances extracted from 5,000 images of 50 specimens. When tested with 5-fold cross-validation algorithm, this early cancer detecting method resulted in the correct classification of over 97% of the cell nucleus. All cancerous positive specimens were successfully detected in the experiment.