Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection and Biosensor Application of Aptamers for Small Molecules

Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
Meta-analyses of studies of 0.2% delmopinol mouth rinse as an adjunct to gingival health and plaque control measures.

BACKGROUND Delmopinol is a third-generation anti-plaque agent used as a mouthwash to reduce plaque and alleviate gingivitis. OBJECTIVE To create an overview of the anti-plaque efficacy of 0.2% delmopinol as an adjunct to normal oral hygiene measures by meta-analysis of completed clinical trials. MATERIALS AND METHODS Eight double-blind, parallel-group studies were identified. Study durations ranged from 8 to 24 weeks. Five studies (n=913) involved supervised rinsing; three studies (n=467) involved unsupervised rinsing. These sets of trials were analysed separately and in combination. Efficacy outcomes comprised modified plaque index, modified gingival index (MGI) and gingival bleeding on probing (BOP). RESULTS Delmopinol 0.2% was superior to placebo for the reduction of plaque scores in both sets of studies. Effects on MGI and BOP were also better with delmopinol 0.2% than with placebo. In most instances, 95% confidence intervals were wholly in favour of delmopinol. Pooled analysis of all eight studies confirmed statistically significant effects of delmopinol 0.2% compared with placebo (p<0.00001). Delmopinol met the efficacy criteria of the American Dental Association in studies of extended duration. CONCLUSION Delmopinol 0.2% mouthwash is effective as an adjunct measure for reducing plaque burden and indices of gingivitis, whether or not it is used under supervision.
MKL-RT: Multiple Kernel Learning for Ratio-trace Problems via Convex Optimization

In the recent past, automatic selection or combination of kernels (or features) based on multiple kernel learning (MKL) approaches has been receiving significant attention from various research communities. Though MKL has been extensively studied in the context of support vector machines (SVM), it is relatively less explored for ratio-trace problems. In this paper, we show that MKL can be formulated as a convex optimization problem for a general class of ratio-trace problems that encompasses many popular algorithms used in various computer vision applications. We also provide an optimization procedure that is guaranteed to converge to the global optimum of the proposed optimization problem. We experimentally demonstrate that the proposed MKL approach, which we refer to as MKL-RT, can be successfully used to select features for discriminative dimensionality reduction and cross-modal retrieval. We also show that the proposed convex MKL-RT approach performs better than the recently proposed non-convex MKL-DR approach.
Optimization of self set and detector generation base on Real-value negative selection algorithm

The Artificial Immune System (AIS) community has been vibrant and active for a number of years now. Artificial Immune Systems (AIS) are a type of intelligent algorithm inspired by the principles and rocesses of the human immune system. Aplications of AIS have been studied in various fields. In the application of anomaly detection, negative selection algorithms of AIS have been successfully applied. Real-valued Negative selection algorithms generate their detector sets based on the points of self data. This paper mainly focuses on self set existing problems and solutions. definite the detector radius according to self radius, and propose negative selection algorithm which is decided by detector radius according to self radius, this way of improved RNS may avoid the detector boundary cross problem. Experiments show that the effect of self region optimized is prominent, and performances of detectors is highly efficient.
Differential distribution of inward rectifier potassium channel transcripts in human atrium versus ventricle.

BACKGROUND The inward rectifier K+ current (IK1) plays an important role in governing cardiac electrical activity and is well known to have different properties in the atrium compared with the ventricle. Several inward rectifier K+ channel (IRK) subunits (hIRK, HH-IRK1, HIR, and TWIK-1) with different properties have been cloned from human tissues, but their relative expression in cardiac tissues has not been quantified. The present study was designed to define the relative levels of mRNA for various IRKs in human atrium and in failing and nonfailing ventricle. METHODS AND RESULTS Competitive reverse transcription-polymerase chain reaction was used to quantify in human atrium and ventricle the mRNA levels of hIRK, HH-IRK1, HIR, and TWIK-1. The absence of important noncardiac contamination was confirmed by demonstrating a lack of detectable mRNA markers for neuronal (acetylcholine receptor) and vascular (maxi-K channel) tissue. mRNA of HIR was more abundant in normal atrium (7.1+/-1.3 amol/ microg total RNA) than ventricle (0.6+/-0.1 amol/ microg, P<0. 05), whereas TWIK-1 mRNA was more concentrated in ventricle (18. 1+/-4.3 amol/ microg) than atrium (1.4+/-0.3 amol/ microg, P<0.05). Concentrations of hIRK (42.7+/-6.7 amol/ microg in atrium vs 57. 1+/-9.2 amol/ microg in ventricle) and HH-IRK1 (2.0+/-0.5 amol/ microg in atrium vs 1.5+/-0.5 amol/ microg in ventricle) were comparable. No significant differences in IRK subunit transcript concentrations were found between normal and failing ventricles. CONCLUSIONS mRNAs for all 4 IRKs are detected in human atrium and ventricle, but the mRNA copy number of a low-conductance subunit (HIR) is larger in atrium and the copy number of a weakly rectifying subunit (TWIK-1) is larger in ventricle. These differences in relative message levels may provide a potential molecular basis for different properties of IK1 in human atrium compared with ventricle.
Visualizing Neuronal Network Connectivity with Connectivity Pattern Tables

Complex ideas are best conveyed through well-designed illustrations. Up to now, computational neuroscientists have mostly relied on box-and-arrow diagrams of even complex neuronal networks, often using ad hoc notations with conflicting use of symbols from paper to paper. This significantly impedes the communication of ideas in neuronal network modeling. We present here Connectivity Pattern Tables (CPTs) as a clutter-free visualization of connectivity in large neuronal networks containing two-dimensional populations of neurons. CPTs can be generated automatically from the same script code used to create the actual network in the NEST simulator. Through aggregation, CPTs can be viewed at different levels, providing either full detail or summary information. We also provide the open source ConnPlotter tool as a means to create connectivity pattern tables.
PSHAe (Probabilistic Seismic Hazard Assessment enhanced): the case of Istanbul

The Probabilistic Seismic Hazard Analysis (PSHA) only relying on ground motion prediction equations (GMPEs) tends to be insufficiently constrained at short distances and data only partially account for the rupture process, seismic wave propagation and three-dimensional (3D) complex configurations. Given a large and representative set of ground shaking scenarios from 3D physics-based numerical simulations, analyzing the resulting database from a statistical point of view and implementing the results as a generalized attenuation function (GAF) into the classical PSHA might be an appealing way to deal with this problem [1]. Nonetheless, the limited amount of computational resources or time available tend to pose substantial constraints to a broad application of the previous method. Furthermore, the method is only partially suitable for taking into account the spatial correlation of ground motion as modelled by each forward physics-based simulation (PBS). In this context, we envision a streamlined and novel approach for enhanced PSHA (“PSHAe”) in large urban areas, alternative to the previous method, based on the integration into the probabilistic framework of a limited number of deterministic scenarios, being the latter wisely chosen and associated to a probability of occurrence. The experience gathered in the past year regarding 3D modelling of seismic wave propagation in complex alluvial basin (see e.g.: [2], [3] and [4]) allowed us to enhance the choice of simulated scenarios in order to explore the variability of ground motion, preserving the full spatial correlation necessary for risk modelling. 3D numerical modelling of scenarios occurring along the North Anatolian Fault in the proximity of Istanbul are carried out through the spectral element code SPEED (http://speed.mox.polimi.it). The results are introduced in a PSHA based code, exploiting the capabilities of this methodology.
The anthropocene and the long seventeenth century: 1550-1750

This chapter investigates the emergence of the Anthropocene by considering some of the dynamics between European cultural values and natural history in early modernity, and their relations with climate change. In particular, it seeks to disentangle the ways in which certain social processes that emerged in the long seventeenth century from 1550 to 1750 not only exacerbated global climate change, but also provided a robust foundation for ecocritical responses to the advance of global climate change in the twenty first century.
Bird communities in the buffer lands of Epping Forest

A farmland site in the green-belt buffer lands to the north of Epping Forest was surveyed for bird species across one calendar year. This is the first known effort in this area. The principal focus was upon birds listed on the Farmland Bird Index, but all species encountered were recorded, giving 41 species in total. Diversity and dominance data is presented for the whole year and across seasons. Eleven of the 19 indicator species were registered, and ten of those were present during breeding season. The majority of the missing eight species are red listed and in population decline, but so are some of those recorded. Generalist species were more readily registered. Woodpigeon is the dominant species, from two forms of analysis. The limitations of this survey and next steps are discussed.
Global and Local Features of Semantic Networks: Evidence from the Hebrew Mental Lexicon

Background Semantic memory has generated much research. As such, the majority of investigations have focused on the English language, and much less on other languages, such as Hebrew. Furthermore, little research has been done on search processes within the semantic network, even though they are abundant within cognitive semantic phenomena. Methodology/Principal Findings We examine a unique dataset of free association norms to a set of target words and make use of correlation and network theory methodologies to investigate the global and local features of the Hebrew lexicon. The global features of the lexicon are investigated through the use of association correlations – correlations between target words, based on their association responses similarity; the local features of the lexicon are investigated through the use of association dependencies – the influence words have in the network on other words. Conclusions/Significance Our investigation uncovered Small-World Network features of the Hebrew lexicon, specifically a high clustering coefficient and a scale-free distribution, and provides means to examine how words group together into semantically related ‘free categories’. Our novel approach enables us to identify how words facilitate or inhibit the spread of activation within the network, and how these words influence each other. We discuss how these properties relate to classical research on spreading activation and suggest that these properties influence cognitive semantic search processes. A semantic search task, the Remote Association Test is discussed in light of our findings.
Optimal Design of Genetic Studies of Gene Expression With Two-Color Microarrays in Outbred Crosses

Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type of study is high. For those organisms where recombinant inbred lines are available for mapping, the “distant pair design” maximizes the number of informative contrasts over all marker loci. Here, we describe an extension of this design, named the “optimal pair design,” for use with F2 crosses between outbred lines. The performance of this design is investigated by simulation and compared to several other two-color microarray designs. We show that, for a given number of microarrays, the optimal pair design outperforms all other designs considered for detection of expression quantitative trait loci (eQTL) with additive effects by linkage analysis. We also discuss the suitability of this design for outbred crosses in organisms with large genomes and for detection of dominance.
A Quantitative Assessment of Forest Cover Change in the Moulouya River Watershed (Morocco) by the Integration of a Subpixel-Based and Object-Based Analysis of Landsat Data

A quantitative assessment of forest cover change in the Moulouya River watershed (Morocco) was carried out by means of an innovative approach from atmospherically corrected reflectance Landsat images corresponding to 1984 (Landsat 5 Thematic Mapper) and 2013 (Landsat 8 Operational Land Imager). An object-based image analysis (OBIA) was undertaken to classify segmented objects as forested or non-forested within the 2013 Landsat orthomosaic. A Random Forest classifier was applied to a set of training data based on a features vector composed of different types of object features such as vegetation indices, mean spectral values and pixel-based fractional cover derived from probabilistic spectral mixture analysis). The very high spatial resolution image data of Google Earth 2013 were employed to train/validate the Random Forest classifier, ranking the NDVI vegetation index and the corresponding pixel-based percentages of photosynthetic vegetation and bare soil as the most statistically significant object features to extract forested and non-forested areas. Regarding classification accuracy, an overall accuracy of 92.34% was achieved. The previously developed classification scheme was applied to the 1984 Landsat data to extract the forest cover change between 1984 and 2013, showing a slight net increase of 5.3% (ca. 8800 ha) in forested areas for the whole region.
Radiographic Markers of Femoroacetabular Impingement: Correlation of Herniation Pit and Femoral Bump with a Positive Cross-Over Ratio

Introduction. The goal of this study was to research the association of femoral bumps and herniation pits with the overlap-ratio of the cross-over sign. Methods. Pelvic X-rays and CT-scans of 2925 patients with good assessment of the anterior and the posterior acetabular wall and absence of neutral pelvic tilt were enrolled in the investigation. Finally pelvic X-rays were assessed for the presence of a positive cross-over sign, and CT-scans for a femoral bump or a herniation pit. Additionally, if a positive cross-over sign was discovered, the overlap-ratio was calculated. Results. A femoral bump was found in 53.3% (n = 1559), and a herniation pit in 27.2% (n = 796) of all hips. The overlap-ratio correlated positively with the presence of a femoral bump, while a negative correlation between the overlap-ratio and the presence of a herniation pit was found. The latter was significantly more often combined with a femoral bump than without. Conclusions. We detected an increased prevalence of femoral bump with increasing overlap-ratios of the cross-over sign indicating a relation to biomechanical stress. The observed decreased prevalence of herniation pits with increasing overlap-ratios could be explained by reduced mechanical stress due to nontightened iliofemoral ligament in the presence of retroversion of the acetabulum.
Point Mutations in Helicobacter pylori's fur Regulatory Gene that Alter Resistance to Metronidazole, a Prodrug Activated by Chemical Reduction

Background Helicobacter pylori's Fur regulatory protein controls transcription of dozens of genes in response to iron availability, acidity and oxidative stress, and affects the vigor of infection and severity of disease. It is unusual among Fur family proteins in being active both when iron-loaded and iron-free. Metholodolgy/Principal Findings We tested if H. pylori fur mutations could affect resistance to metronidazole (Mtz), an anti-H. pylori prodrug rendered bactericidal by chemical reduction. Point mutations were made by PCR in DNA containing fur and a downstream chloramphenicol resistance gene, and were placed in the H. pylori chromosome by transformation of a fur-deletion (Δfur) strain. Several substitutions affecting H. pylori Fur's ∼10 residue N terminal arm, which has no counterpart in prototype (E. coli-type) Fur proteins, increased Mtz resistance, as did mutations affecting the region between DNA binding and dimerization domains. Three types of mutations decreased resistance more than did Δfur: substitutions affecting the N-terminal arm; substitutions affecting the metal binding pocket; and nonsense mutations that resulted in a truncated Fur protein with no C-terminal dimerization domain. Most metal binding pocket mutations were obtained only in fur genes with additional inactivating mutations, and thus seemed deleterious or lethal because they. Conclusions/Significance These results establish that H. pylori Fur's distinctive N terminal arm is functional, and more generally illustrate that point mutations can confer informative phenotypes, distinct from those conferred by null mutations. We propose that fur mutations can affect Mtz susceptibility by altering the balance among Fur's several competing activities, and thereby the expression of genes that control cellular redox potential or elimination of bactericidal Mtz activation products. Further analyses of selected mutants should provide insights into Fur interactions with other cellular components, metabolic circuitry, and how H. pylori thrives in its special gastric niche.
Hardware-assisted view-dependent map simplification

In this paper, we present an algorithm and a system to perform dynamic view dependent simplification of large geographical maps through a novel use of graphics hardware. Given a map as a collection of non-intersecting chains and a tolerance parameter for each chain, we produce a simplified map that resembles the original map, satisfying the condition that the distance between each point on the simplified chain and the original chain is within the given tolerance parameter, and that no two chains intersect. We also present an interactive map visualization system which uses frame-to-frame coherence to perform dynamic view-dependent simplification. Our initial results indicate that we get a 3-4 fold increase in the frame rates using our simplification algorithm on maps with 1.5-2 million vertices on an SGI Onyx workstation.
Recursive complexity of the Carnap first order modal logic C

We consider first order modal logic C firstly defined by Carnap in “Meaning and Necessity” [1]. We prove elimination of nested modalities for this logic, which gives additionally the Skolem‐Löwenheim theorem for C. We also evaluate the degree of unsolvability for C, by showing that it is exactly 0′. We compare this logic with the logics of Henkin quantifiers, Σ11 logic, and SO. We also shortly discuss properties of the logic C in finite models. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Nonparametric Bayesian Double Articulation Analyzer for Direct Language Acquisition From Continuous Speech Signals

Human infants can discover words directly from unsegmented speech signals without any explicitly labeled data. Current machine learning methods cannot efficiently estimate language model (LM) and acoustic model (AM) and discover words directly from continuous human speech signals in an unsupervised manner. To solve this problem, we propose an integrative generative model that combines an LM and an AM into a single generative model called the hierarchical Dirichlet process hidden LM (HDP-HLM). The HDP-HLM is obtained by extending the hierarchical Dirichlet process hidden semi-Markov model (HDP-HSMM) proposed by Johnson et al. An inference procedure for the HDP-HLM is derived using the blocked Gibbs sampler originally proposed for the HDP-HSMM. This procedure enables the simultaneous and direct inference of LM and AM from continuous speech signals. Based on the HDP-HLM and its inference procedure, we develop a novel machine learning method called nonparametric Bayesian double articulation analyzer (NPB-DAA) that can directly acquire LM and AM from observed continuous speech signals. By assuming HDP-HLM as a generative model of observed time series data, and by inferring latent variables of the model, the method can analyze latent double articulation structure, i.e., hierarchically organized latent words and phonemes, of the data in an unsupervised manner. We also carried out two evaluation experiments using synthetic data and actual human continuous speech signals representing Japanese vowel sequences. In the word acquisition and phoneme categorization tasks, the NPB-DAA outperformed a conventional double articulation analyzer and baseline automatic speech recognition system whose AM was trained in a supervised manner. The main contributions of this paper are as follows: 1) we develop a probabilistic generative model that integrates LM and AM, i.e., HDP-HLM; 2) we derive an inference method for this, and propose the NPB-DAA; and 3) we show that the NPB-DAA can discover words directly from continuous human speech signals in an unsupervised manner.
Dynamic Interactions between Goals and Beliefs

Shapiro et al. [2005; 2006], presented a framework for representing goal change in the situation calculus. In that framework, agents adopt a goal when requested to do so (by some agent reqr), and they remain committed to the goal unless the request is cancelled by reqr. A common assumption in the agent theory literature, e.g., [Cohen and Levesque, 1990; Rao and Georgeff, 1991], is that achievement goals that are believed to be impossible to achieve should be dropped. In this paper, we incorporate this assumption into Shapiro et al.'s framework, however we go a step further. If an agent believes a goal is impossible to achieve, it is dropped. However, if the agent later believes that it was mistaken about the impossibility of achieving the goal, the agent might readopt the goal. In addition, we consider an agent's goals as a whole when making them compatible with their beliefs, rather than considering them individually.
Teaching Imperative Programming With Contracts at the Freshmen Level

We describe the experience with a freshmen-level course that teaches imperative programming and methods for ensuring the correctness of programs. Students learn the process and concepts needed to go from high-level descriptions of algorithms to correct imperative implementations, with specific applications to basic data structures and algorithms. A novel aspect of the course is that much of it is conducted in C0, a small safe subset of the C programming language, augmented with a layer of annotations to express contracts that are amenable to verification. The present version of the course assumes a basic understanding of programming (variables, expressions, loops, functions) and prepares students for subsequent computer systems courses taught in C as well as more advanced courses on algorithms and data structures.