Miracle-dz/UniFAR-FTUs huggingface dataset:
Preclinical Validation of Novel Fluorescently Labeled Compounds to Treat Neurodegenerative Hearing Loss

Introduction: As otology enters the field of gene therapy and human studies commence, the question arises whether audiograms e the current gold standard for the evaluation of hearing function e can consistently predict cellular damage within the human inner ear and thus should be used to define inclusion criteria for trials. Current assumptions rely on the analysis of small groups of human temporal bones post mortem or from psychophysical identification of cochlear “dead regions” in vivo, but a comprehensive study assessing the correlation between audiometric thresholds and cellular damage within the cochlea is lacking. Methods: A total of 131 human temporal bones from 85 adult individuals (ages 19e92 years, median 69 years) with sensorineural hearing loss due to various etiologies were analyzed. Cytocochleograms e which quantify loss of hair cells, neurons, and strial atrophy along the length of the cochlea e were compared with subjects' latest available audiometric tests prior to death (time range 5 he22 years, median 24 months). The Greenwood function and the equivalent rectangular bandwidth were used to infer, from cytocochleograms, cochlear locations corresponding to frequencies tested in clinical audiograms. Correlation between audiometric thresholds at clinically tested frequencies and cell type-specific damage in those frequency regions was examined by calculating Spearman's correlation coefficients. Results: Similar audiometric profiles reflected widely different cellular damage in the cochlea. In our diverse group of patients, audiometric thresholds tended to be more influenced by hair cell loss than by neuronal loss or strial atrophy. Spearman's correlation coefficient across frequencies was at most 0.7 and often below 0.5, with 1.0 indicating perfect correlation. Conclusions: Audiometric thresholds do not predict specific cellular damage in the human inner ear. Our study highlights the need for better nonor minimally-invasive tools, such as cochlear endoscopy, to establish cellular-level diagnosis and thereby guide therapy and monitor response to treatment. © 2016 Elsevier B.V. All rights reserved.
What Is a Structural Representation in Chemistry: Towards a Unified Framework for CADD?

A fundamentally new formal framework for structural representation of organic compounds based on the rst \true" (general) formalism for structural object representation recently proposed by us|evolving transformation system (ETS) model|is outlined. The applied orientation of the paper is towards the molecular design in general and computer aided drug design (CADD) in particular. Inadequacies of the conventional models used in (CADD) for molecular representation and classi cation as well as the advantages of the proposed ETS model are discussed. Some advantages of the ETS model is its capability to represent naturally all important structural features of molecules, e.g. di erent atoms and their bonding types (including hydrogen bonding), basic 2D and 3D isometries, the molecular class structure. The model allows one not only to classify a new compound, but also to construct a chemically valid new compound from the class of compounds that was previously learned based on a small set of examples. The model also guarantees the inheritance of the chemical structural class information from the parent class to all its subclasses. In general, the ETS model o ers a much more precise \language" for chemical structural formulas. The central role of the class learning problem in CADD is suggested. Moreover, we propose the ETS model as a uni ed framework for the class learning problem and therefore as a uni ed formal framework for CADD. This would allow considerable streamlining of the CADD by assigning to the chemist the role of an interactive user of the system rather that a role of a human weak link within the CADD process. To whom correspondence should be addressed (tel: 506-458-7271, e-mail: goldfarb@unb.ca)
The above‐ground coarse wood productivity of 104 Neotropical forest plots

The net primary production of tropical forests and its partitioning between long‐lived carbon pools (wood) and shorter‐lived pools (leaves, fine roots) are of considerable importance in the global carbon cycle. However, these terms have only been studied at a handful of field sites, and with no consistent calculation methodology. Here we calculate above‐ground coarse wood carbon productivity for 104 forest plots in lowland New World humid tropical forests, using a consistent calculation methodology that incorporates corrections for spatial variations in tree‐size distributions and wood density, and for census interval length. Mean wood density is found to be lower in more productive forests. We estimate that above‐ground coarse wood productivity varies by more than a factor of three (between 1.5 and 5.5 Mg C ha−1 a−1) across the Neotropical plots, with a mean value of 3.1 Mg C ha−1 a−1. There appear to be no obvious relationships between wood productivity and rainfall, dry season length or sunshine, but there is some hint of increased productivity at lower temperatures. There is, however, also strong evidence for a positive relationship between wood productivity and soil fertility. Fertile soils tend to become more common towards the Andes and at slightly higher than average elevations, so the apparent temperature/productivity relationship is probably not a direct one. Coarse wood productivity accounts for only a fraction of overall tropical forest net primary productivity, but the available data indicate that it is approximately proportional to total above‐ground productivity. We speculate that the large variation in wood productivity is unlikely to directly imply an equivalent variation in gross primary production. Instead a shifting balance in carbon allocation between respiration, wood carbon and fine root production seems the more likely explanation.
Controlling Voltages and Reduction of Real Power Loss in Power System by Using Crossbreed Spiral Dynamics Bacterial Chemotaxis Algorithm

In this paper a new hybrid optimization algorithm, referred to as Crossbreed spiral dynamics bacterial chemotaxis algorithm (CSDBCA) is proposed to solve the optimal reactive power dispatch (ORPD) Problem. CSDBCA synergizes bacterial foraging algorithm (BFA) chemotaxis approach and spiral dynamics algorithm (SDA). The original BFA has higher convergence speed while SDA has better accuracy and stable convergence when approaching the optimum value. This crossbreed approach conserves the strengths of BFA and SDA. So the CSDBCA has the capability of producing superior results. In order to evaluate the proposed algorithm, it has been tested on IEEE 30 bus system consisting 6 generators and compared other algorithms and simulation results show that CSDBCA is more efficient than others in solving the reactive power dispatch problem.
Biological Control of Root Pathogens by Plant- Growth Promoting Bacillus spp.

At the present time, among the most important factors limiting production of different crops are soil-borne plant pathogens [1]. Which include the genera Pythium, Rhizoctonia, Fusarium, Verticillium, Phytophthora spp, Sclerotinia, Sclerotium, and Rosellinia [2]. By this reason, different methods have been used to control these pathogens [3]. Cultural practi‐ ces and chemical control using synthetic fungicides are the most used control methods [4], however, use of some of these synthetic products has caused various problems due to environmental pollution, with consequences such as toxicity to humans, as well as re‐ sistance of certain pathogens to these fungicides [5]. An alternative to reduce the effect of these plant pathogens is the use of antagonistic microorganisms such as: some species of the genusBacillus which is recognized as one of the most effective biological control agent because of their properties on pathogens growth inhibition [6-7]. Biological control has many advantages as an alternative in the integrated management of diseases such as little or no harmful side effects, rare cases of resistance, long-term control, completely or substantially eliminates the use of synthetic pesticides, cost / benefit ratio very favorable; prevents secondary diseases, not symptoms of poisoning and can be used as part of inte‐ grated disease management [8]. Generally, the mode of action of Bacillus is antibiosis by producing extracellular hydrolytic enzymes which decompose polysaccharides, nucleic acids, other way are: production of antibiotics such as bacitracin, polymyxin, and grami‐ cidin, [9-11], competition to occupy an ecological niche and metabolize root exudates on pathogens affecting their growth [12-13]. Also, activating plant resistance induction when
THE TEMPERATURE–DENSITY RELATION IN THE INTERGALACTIC MEDIUM AT REDSHIFT 〈z〉 = 2.4

We present new measurements of the temperature–density (T–ρ) relation for neutral hydrogen in the 2.0 < z < 2.8 intergalactic medium (IGM) using a sample of ∼6000 individual H i absorbers fitted with Voigt profiles constrained in all cases by multiple Lyman series transitions. We find model-independent evidence for a positive correlation between the column density of H i (NH i) and the minimum observed velocity width of absorbers (bmin). With minimal interpretation, this implies that the T–ρ relation in the IGM is not “inverted,” contrary to many recent studies. Fitting bmin as a function of NH i results in line-width–column-density dependence of the form bmin = b0(NH i/NH i,0)Γ−1 with a minimum line width at mean density ( cm−2) of b0 = 17.9 ± 0.2 km s−1 and a power-law index of (Γ − 1) = 0.15 ± 0.02. Using analytic arguments, these measurements imply an “equation of state” for the IGM at 〈z〉 = 2.4 of the form with a temperature at mean density of T0 = [1.94 ± 0.05] × 104 K and a power-law index (γ − 1) = 0.46 ± 0.05.
(PANEL ON EDUCATION IN SIMULATION)

This panel discusses goals and educational strategies for teaching simulation in academia. Clearly, there is considerable material to cover in a single course or a sequence thereof in, say, an undergraduate program. The issue is how to motivate and empower students to analyze complex problems correctly and to prevent the pitfall of misusing the concept.
Exploring Deployment Strategies for the Tor Network [Extended Version]

In response to upcoming performance and security challenges of anonymity networks like Tor, it will be of crucial importance to be able to develop and deploy performance improvements and state-of-the-art countermeasures. In this paper, we therefore explore different deployment strategies and review their applicability to the Tor network. In particular, we consider flag day, dual stack, translation, and tunneling strategies and discuss their impact on the network, as well as common risks associated with each of them. In a simulation based evaluation, which stems on historical data of Tor, we show that they can practically be applied to realize significant protocol changes in Tor. However, our results also indicate that during the transitional phase a certain degradation of anonymity is unavoidable with current viable deployment strategies. Keywords—Internet security, overlay networks
Regulation of phytoplankton carbon to chlorophyll ratio by light, nutrients and temperature in the Equatorial Pacific Ocean: a basin-scale model

Abstract. The complex effects of light, nutrients and temperature lead to a variable carbon to chlorophyll (C:Chl) ratio in phytoplankton cells. Using field data collected in the Equatorial Pacific, we derived a new dynamic model with a non-steady C:Chl ratio as a function of irradiance, nitrate, iron, and temperature. The dynamic model is implemented into a basin-scale ocean circulation-biogeochemistry model and tested in the Equatorial Pacific Ocean. The model reproduces well the general features of phytoplankton dynamics in this region. For instance, the simulated deep chlorophyll maximum (DCM) is much deeper in the western warm pool (~100 m) than in the Eastern Equatorial Pacific (~50 m). The model also shows the ability to reproduce chlorophyll, including not only the zonal, meridional and vertical variations, but also the interannual variability. This modeling study demonstrates that combination of nitrate and iron regulates the spatial and temporal variations in the phytoplankton C:Chl ratio in the Equatorial Pacific. Sensitivity simulations suggest that nitrate is mainly responsible for the high C:Chl ratio in the western warm pool while iron is responsible for the frontal features in the C:Chl ratio between the warm pool and the upwelling region. In addition, iron plays a dominant role in regulating the spatial and temporal variations of the C:Chl ratio in the Central and Eastern Equatorial Pacific. While temperature has a relatively small effect on the C:Chl ratio, light is primarily responsible for the vertical decrease of phytoplankton C:Chl ratio in the euphotic zone.
Comparative evidence for strong phylogenetic inertia in precloacal signalling glands in a species-rich lizard clade

Background: The precloacal glands of lizards are responsible for the secretion of pheromones involved in chemical-based interactions, such as male territoriality and female mate choice. However, in spite of the significance of these structures for social and sexual communication, their evolution remains poorly studied. Previous research has suggested that the number of precloacal glands may reflect adaptive variation because a higher number of these organs increases the potential rate of secretion, compensating for the impact of extreme environmental conditions on the optimal quantity of secretions smeared on the substrate. Therefore, the number of precloacal glands may be expected to exhibit convergent evolution in response to similar environments. Nevertheless, the only available evidence testing this prediction ignored potential effects of shared phylogenetic history on the evolution of this trait. Hypotheses: (1) Lizard precloacal gland number evolves adaptively in response to variation in environmental conditions, experiencing convergent patterns independent of phylogenetic relationships. (2) Species with a wider geographical distribution exhibit higher variance in the number of precloacal glands as a response to variation along environmental gradients. Organisms: Liolaemus lizards, one of the largest and most ecologically diverse vertebrate genera. Methods: Phylogenetic comparative methods. Regression analyses based on phylogenetic independent contrasts, and on raw data at intra-clade level. Historical estimates based on ancestral state reconstructions from explicit phylogenetic hypotheses. Results: Precloacal glands are constrained by phylogenetic relationships. In contrast to previous work, we found no evidence for independent convergent events along the phylogenetic history of this lineage. Environmental conditions failed to predict the number of glands in species of the Liolaemus genus in both current and reconstructed ancestral states. Conclusions: Our phylogenetically controlled comparative analysis fails to support the hypothesis that the number of precloacal emitter glands in lizards is the product of adaptive evolution.
Probing the chiral nature of electromagnetic fields surrounding plasmonic nanostructures

We investigate the chiral properties of near fields around plasmonic nanostructures and their relation to the electromagnetic chirality C. By combining chiral metal nanoparticles with achiral dye molecules and measuring the circular polarization dependence of the enhanced photoluminescence, we find a correlation between the dissymmetry of the luminescence enhancement and the calculated values of C. These effects are strong (∼10 −1 ), despite the weak circular dichroism of the particles (∼10 −5 ). We further show that C represents the chiral selectivity of the near-field coupling between an emitter and a nanoantenna.
Causal Mediation in a Survival Setting with Time-Dependent Mediators

The effect of an expsore on an outcome of interest is often mediated by intermediate variables. The goal of causal mediation analysis is to evaluate the role of these intermediate variables (mediators) in the causal effect of the exposure on the outcome. In this paper, we consider causal mediation of a baseline exposure on a survival (or time-to-event) outcome, when the mediator is time-dependent. The challenge in this setting lies in that the event process takes places jointly with the mediator process; in particular, the length of the mediator history depends on the survival time. As a result, we argue that the definition of natural effects in this setting should be based on only blocking those paths from treatment to mediators that are not through the survival history. We propose to use a stochastic interventions (SI) perspective, introduced by Didelez, Dawid, and Geneletti (2006), to formulate the causal mediation analysis problem in this setting. Under this formulation, the mediators are regarded as intervention variables, onto which a given counterfactual distribution is enforced. The natural direct and indirect effects can be defined analogously to the ideas in Pearl (2001). In particular, they also allow for a total effect decomposition and an interpretation of the natural direct effect as a weighted average of controlled direct effects. The statistical parameters that should arise are defined nonparametrically; therefore, they have meaningful interpretations, independent of the causal formulations and assumptions. We present a general semiparametric inference framework for these parameters. Using their efficient influence functions, we develop semiparametric efficient and robust targeted substitution-based (TMLE) and estimating-equation-based (A-IPTW) estimators. An IPTW estimator and g-computation estimator will also be presented.
Analysis on Influencing Factors Identification of Crash Rates Using Tobit Model with Endogenous Variable

The objective of this study is to identify the influencing factors of crash rates from the perspective of access management techniques in urban areas. The target areas are located in the Las Vegas Metropolitan area, and 19 arterials are selected. In order to address the interdependency between crash rates and travel speeds, and left-censored issue, a tobit model with endogenous variable is presented. The structure of the tobit model addresses the left-censored issue for the segments meanwhile the endogeneity issue between crash rates and travel speeds is explained. The results indicate that there is a strong interdependency between crash rates and travel speeds. The segment length, driveway density, median opening density, posted speed limit and AADT per lane are statistically significant factors that influence crash rates on segments, moreover, crash rates are significantly influenced by two-directional median opening density.
Analgesic and anti-diarrhoeal activities of Lagerstroemia speciosa roots in experimental animal model

The methanolic crude extract of Lagerstroemia speciosa roots was investigated for its possible analgesic and anti-diarrhoeal activities in experimental animal model. Phytochemical screening of the methanolic extract of L. speciosa roots showed the presence of alkaloids, flavonoids, saponins, tannins and reducing sugar. In acute toxicity study, no mortality or toxic reaction was recorded in animal model after administration of the L. speciosa roots extract. Analgesic activity was evaluated by using acetic acid induced writhing inhibition method in Swiss albino mice. In peripheral method of anti-nociception, the methanolic crude extract of L. speciosa roots showed significant analgesic activity. At the dose of 200 and 400 mg/kg body weight, the extract produced 35.38% and 53.85% (P<0.001) of writhing inhibition, respectively compared to standard diclofenac sodium (70.77% inhibition). The extract had also anti-diarrhoeal activity in castor oil induced method and inhibited the mean number of defecation by 32.75% (P<0.01) and 51.72 % (P<0.001) at the dose of 200 and 400 mg/kg body weight, respectively. The latent period for the extract treated group also increased significantly. DOI: http://dx.doi. org/10.3329/dujps.v13i1. 21860 Dhaka Univ. J. Pharm. Sci. 13(1): 57-62, 2014 (June)
Nigella sativa OIL COULD INDUCE OSTEOGENIC DIFFERENTIATION OF DENTAL PULP MESENCHYMAL STEM CELLS: CLINICAL NUTRITION FOR DENTISTRY

A natural agent that, promotes osteogenic differentiation of dental pulp mesenchymal stem cells (DP-MSCs) could achieve success in regeneration during healing and may also prevent bone resorption and improve regeneration. We aimed to demonstrate that a Nigella sativa oil could induce differentiation of DP-MSCs. DP-MSCs were isolated from 3. molars and identified with flow cytometer. Osteogenic differentiation was conducted, and calcium granules were showed by typical Alizarin Red dying and calcium concentration were determined by DICA 500. Identification results showed that the cells are mesenchymal stem cells. Alizarin Red dying signed the calcium granules and DICA 500 showed that calcium concentrations were higher than the Control Group. This preliminary study shows for the first time the inductive potential of N. sativa oil for osteogenic differentiation in DP-MSCs. The mechanism should be investigated in further studies.
EARTHQUAKE DISASTER PLANNING IN NURSERY SCHOOLS

Disaster management planning of all educational institutes in high earthquake prone-areas is a necessity. In this paper, the development of an earthquake management system for nursery schools is highlighted. The unavoidable nature of the disasters, the impossibility to predict them and the need for considering the safety of the very young generation who are the future assets of communities emphasises this priority. Furthermore, small children are indeed one of the most vulnerable groups of the society, therefore, their protection is considered as highly important. This paper aims to develop an appropriate earthquake disaster management system for Iranian nursery schools with the hope that other developing countries can also benefit from the proposed programme. The plan can be expanded and implemented in schools, high schools and universities subject to specific requirements.
Applications of Covariance Structure Modeling in Psychology : Cause for Concern ?

Methods of covariance structure modeling are frequently applied in psychological research. These methods merge the logic of confirmatory factor analysis, multiple regression, and path analysis within a single data analytic framework. Among the many applications are estimation of disattenuated correlation and regression coefficients, evaluation of multitrait-multimethod matrices, and assessment of hypothesized causal structures. Shortcomings of these methods are commonly acknowledged in the mathematical literature and in textbooks. Nevertheless, serious flaws remain in many published applications. For example, it is rarely noted that the fit of a favored model is identical for a potentially large number of equivalent models. A review of the personality and social psychology literature illustrates the nature of this and other problems in reported applications of covariance structure models.