Miracle-dz/UniFAR-FTUs huggingface dataset:
Variation in Host and Pathogen in the Neonectria/Malus Interaction; toward an Understanding of the Genetic Basis of Resistance to European Canker

Apple canker caused by the phytopathogenic fungus Neonectria ditissima is an economically important disease, which has spread in recent years to almost all pome-producing regions of the world. N. ditissima is able to cross-infect a wide range of apple varieties and causes branch and trunk lesions, known as cankers. Most modern apple varieties are susceptible and in extreme cases suffer from high mortality (up to 50%) in the early phase of orchard establishment. There is no known race structure of the pathogen and the global level of genetic diversity of the pathogen population is unknown. Resistance breeding is underway in many global breeding programmes, but nevertheless, a total resistance to canker has not yet been demonstrated. Here we present preliminary data from a survey of the phylogenetic relationships between global isolates of N. ditissima which reveals only slight evidence for population structure. In addition we report the results of four rapid screening tests to assess the response to N. ditissima in different apple scion and rootstock varieties, which reveals abundant variation in resistance responses in both cultivar and rootstock material. Further seedling tests show that the segregation patterns of resistance and susceptibility vary widely between crosses. We discuss inconsistencies in test performance with field observations and discuss future research opportunities in this area.
Estimating Risk from Ambient Concentrations of Acrolein across the United States

Background Estimated ambient concentrations of acrolein, a hazardous air pollutant, are greater than the U.S. Environmental Protection Agency (EPA) reference concentration throughout the United States, making it a concern for human health. However, there is no method for assessing the extent of risk under the U.S. EPA noncancer risk assessment framework. Objectives We estimated excess risks from ambient concentrations of acrolein based on dose–response modeling of a study in rats with a relationship between acrolein and residual volume/total lung capacity ratio (RV/TLC) and specific compliance (sCL), markers for altered lung function. Methods Based on existing literature, we defined values above the 90th percentile for controls as “adverse. ” We estimated the increase over baseline response that would occur in the human population from estimated ambient concentrations of acrolein, taken from the U.S. EPA’s National-Scale Air Toxics Assessment for 1999, after standard animal-to-human conversions and extrapolating to doses below the experimental data. Results The estimated median additional number of adverse sCL outcomes across the United States was approximately 2.5 cases per 1,000 people. The estimated range of additional outcomes from the 5th to the 95th percentile of acrolein concentration levels across census tracts was 0.28–14 cases per 1,000. For RV/TLC, the median additional outcome was 0.002 per 1,000, and the additional outcome at the 95th percentile was 0.13 per 1,000. Conclusions Although there are uncertainties in estimating human risks from animal data, this analysis demonstrates a method for estimating health risks for noncancer effects and suggests that acrolein could be associated with decreased respiratory function in the United States.
Measuring the Strength of Mice

Kondziela7 devised the inverted screen test and published it in 1964. It is a test of muscle strength using all four limbs. Most normal mice easily score maximum on this task; it is a quick but insensitive gross screen, and the weights test described in this article will provide a finer measure of muscular strength. There are also several strain gauge-based pieces of apparatus available commercially that will provide more graded data than the inverted screen test, but their cost may put them beyond the reach of many laboratories which do not specialize in strength testing. Hence in 2000 a cheap and simple apparatus was devised by the author. It consists of a series of chain links of increasing length, attached to a "fur collector" a ball of fine wire mesh sold for preventing limescale build up in hard water areas. An accidental observation revealed that mice could grip these very tightly, so they proved ideal as a grip point for a weight-lifting apparatus. A common fault with commercial strength meters is that the bar or other grip feature is not thin enough for mice to exert a maximum grip. As a general rule, the thinner the wire or bar, the better a mouse can grip with its small claws. This is a pure test of strength, although as for any test motivational factors could potentially play a role. The use of scale collectors, however, seems to minimize motivational problems as the motivation appears to be very high for most normal young adult mice.
Effects of age and MAOA genotype on the neural processing of social rejection

Adolescents are often sensitive to peer rejection, a factor that might contribute to the risk of affective disorder in this age group. Previous studies suggest a significant overlap among socioaffective brain regions involved in the response to social rejection, regions continuing to develop functionally during adolescence and regions influenced by monoamine oxidase A (MAOA) polymorphism. The current study investigated whether the neural response to social rejection is functionally immature in adolescents compared with adults, and whether these responses are modulated by MAOA genotype. Blood‐oxygen‐level‐dependent response was measured with functional magnetic resonance imaging during a rejection‐themed emotional Stroop task in 19 adolescents (aged 14–16) and 16 adults (aged 23–28) genotyped for MAOA polymorphism. Similar numbers of MAOA‐L and MAOA‐H carriers were recruited to maximize power to detect genotype effects. Main effects of rejection stimuli (relative to neutral and acceptance control stimuli) were seen in predicted socioaffective brain regions. Adolescents did not show the adult pattern of modulation by rejection stimuli in the right ventrolateral prefrontal cortex, suggesting continued functional maturation of this regulatory region during adolescence. Age and genotype interacted in the left amygdala, in which the predicted effect of genotype on responses to rejection stimuli was seen in the adults, but not in the adolescents. The data suggest continued functional development of the circuitry underlying the processing of social rejection between adolescence and adulthood, and show that the effects of MAOA genotype on neural responses may vary with age.
Improving health in at-risk youth through Photovoice

Photovoice is a practical method to allow at-risk youth to express the environmental influences in their lives at school, at home, and in their community. This project emerged from an interprofessional collaboration between social work and nursing that focused on school health. The purpose was to explore the factors influencing the mental and emotional health using photographs by students in a largely Hispanic middle school. Ten students were recruited and consented but only eight completed the project. The SHOWeD method was used to assist the students to formally reflect upon their photographs. Data analysis was conducted using content analysis to identify themes presented the students’ reflections. The themes were staying healthy, stress dealing with anger/frustration, maintaining friendships and communication, recognizing bullying, and planning for the future. Reflections aided students to provide rich details about how the school environment influences their mental and emotional health. The use of Photovoice is a reasonable method for at-risk youth to explore and describe their environment. Nurses, social workers, parents, and school leaders can use the new knowledge about how the school environment influences the health of students to develop tools to support a healthy school and community environment.
The effect of alendronate soaking and ultraviolet treatment on bone–implant interface

OBJECTIVE Rapid and stable fixation of dental implants is crucial for successful treatment. Herein, we examined whether the simultaneous treatment of titanium implants with ultraviolet (UV) and alendronate (ALN) synergistically improved the bone-to-implant contact. MATERIALS AND METHODS We assessed the in vitro effects of UV radiation-treated (UV+/ALN-), ALN-soaked (UV-/ALN+), and UV radiation/ALN-treated (UV+/ALN+) titanium implants on cell proliferation, cytotoxicity, cell adhesion, and osteoblast differentiation using MG-63 osteoblast-like cells by the assays of MTS, live/dead, scanning electron microscopy (SEM), alkaline phosphatase (ALP) activity, and alizarin red S (AR-S) staining, respectively. Furthermore, in vivo bone formation at the bone-implant interface efficiency determined using a rabbit tibia implantation. Implants were divided into 3 experimental groups (UV+/ALN-, UV-/ALN+, UV+/ALN+) and the non-treated control (UV-/ALN-) group and transplanted into the proximal tibia of rabbits. At 1, 2, 4, and 8 weeks post-operation, bone formation at the bone-implant interface was evaluated by micro-computed tomography and histological analysis. RESULTS MG-63 cells cultured on UV+/ALN+ implants showed significantly higher cell proliferation, ALP activity, and calcium mineralization than those cultured on other implants (P < 0.05). Furthermore, SEM observation showed the highest increase in cell attachment and growth on the UV+/ALN+ implants. In vivo, experimental groups at all time points showed greater peri-implant bone formation than the control group. At 8 weeks post-implantation, in the UV+/ALN+ group, significantly higher bone formation was observed than the UV+/ALN- or UV-/ALN+ group, respectively (P < 0.05). CONCLUSIONS Treatment of titanium surfaces with UV and ALN may synergistically enhance osteoblastic differentiation and mineralization in vitro and enhance bone formation at the bone-implant interface in vivo. These data suggest that UV and ALN treatment may improve the osseointegration of titanium implants.
Frequency tuning and intensity coding of sound in the auditory periphery of the lake sturgeon, Acipenser fulvescens

SUMMARY Acipenser fulvescens, the lake sturgeon, belongs to one of the few extant non-teleost ray-finned (bony) fishes. The sturgeons (family Acipenseridae) have a phylogenetic history that dates back about 250 million years. The study reported here is the first investigation of peripheral coding strategies for spectral analysis in the auditory system in a non-teleost bony fish. We used a shaker system to simulate the particle motion component of sound during electrophysiological recordings of isolated single units from the eighth nerve innervating the saccule and lagena. Background activity and response characteristics of saccular and lagenar afferents (such as thresholds, response–level functions and temporal firing) resembled the ones found in teleosts. The distribution of best frequencies also resembled data in teleosts (except for Carassius auratus, goldfish) tested with the same stimulation method. The saccule and lagena in A. fulvescens contain otoconia, in contrast to the solid otoliths found in teleosts, however, this difference in otolith structure did not appear to affect threshold, frequency tuning, intensity- or temporal responses of auditory afferents. In general, the physiological characteristics common to A. fulvescens, teleosts and land vertebrates reflect important functions of the auditory system that may have been conserved throughout the evolution of vertebrates.
Using linear programming to Decode Binary linear codes

A new method is given for performing approximate maximum-likelihood (ML) decoding of an arbitrary binary linear code based on observations received from any discrete memoryless symmetric channel. The decoding algorithm is based on a linear programming (LP) relaxation that is defined by a factor graph or parity-check representation of the code. The resulting "LP decoder" generalizes our previous work on turbo-like codes. A precise combinatorial characterization of when the LP decoder succeeds is provided, based on pseudocodewords associated with the factor graph. Our definition of a pseudocodeword unifies other such notions known for iterative algorithms, including "stopping sets," "irreducible closed walks," "trellis cycles," "deviation sets," and "graph covers. " The fractional distance d/sub frac/ of a code is introduced, which is a lower bound on the classical distance. It is shown that the efficient LP decoder will correct up to /spl lceil/d/sub frac//2/spl rceil/-1 errors and that there are codes with d/sub frac/=/spl Omega/(n/sup 1-/spl epsi//). An efficient algorithm to compute the fractional distance is presented. Experimental evidence shows a similar performance on low-density parity-check (LDPC) codes between LP decoding and the min-sum and sum-product algorithms. Methods for tightening the LP relaxation to improve performance are also provided.
An Information Systems Model of the Determinants of Electronic Health Record Use

Summary Objectives: The prominence given to universal implementation of electronic health record (EHR) systems in U.S. health care reform, underscores the importance of devising reliable measures of factors that predict medical care providers’ use of EHRs. This paper presents an easily administered provider survey instrument that includes measures corresponding to core dimensions of DeLone and McClean’s (D & M) model of information system success. Methods: Study data came from self-administered surveys completed by 460 primary care providers, who had recently begun using an EHR. Results: Based upon assessment of psychometric properties of survey items, a revised D&M causal model was formulated that included four measures of the determinants of EHR use (system quality, IT support, ease of use, user satisfaction) and five indicators of provider beliefs about the impact on an individual’s clinical practice. A structural equation model was estimated that demonstrated a high level of inter-correlation between the four scales measuring determinants of EHR use. All four variables had positive association with each of the five individual impact measures. Consistent with our revised D&M model, the association of system quality and IT support with the individual impact measures was entirely mediated by ease of use and user satisfaction. Conclusions: Survey research provides important insights into provider experiences with EHR. Additional studies are in progress to investigate how the variables constructed for this study are related to direct measures of EHR use. Citation: Messeri P, Khan S, Millery M, Campbell A, Merrill J, Shih S, Kukafka R. An information systems model of the determinants of electronic health record use. Appl Clin Inf 2013; 4: 185–200 http://dx.doi. org/10.4338/ACI-2013-01-RA-0005
The Tig1 Histone Deacetylase Complex Regulates Infectious Growth in the Rice Blast Fungus Magnaporthe oryzae[C][W][OA]

This study analyzed a transducin β-like gene (TIG1) from the fungal rice pathogen Magnaporthe oryzae. TIG1 was found to interact with several conserved core proteins to form a histone deacetylase complex, which is critical for invasive growth and conidiogenesis in the rice blast fungus. Magnaporthe oryzae is the most damaging fungal pathogen of rice (Oryza sativa). In this study, we characterized the TIG1 transducin β-like gene required for infectious growth and its interacting genes that are required for plant infection in this model phytopathogenic fungus. Tig1 homologs in yeast and mammalian cells are part of a conserved histone deacetylase (HDAC) transcriptional corepressor complex. The tig1 deletion mutant was nonpathogenic and defective in conidiogenesis. It had an increased sensitivity to oxidative stress and failed to develop invasive hyphae in plant cells. Using affinity purification and coimmunoprecipitation assays, we identified several Tig1-associated proteins, including two HDACs that are homologous to components of the yeast Set3 complex. Functional analyses revealed that TIG1, SET3, SNT1, and HOS2 were core components of the Tig1 complex in M. oryzae. The set3, snt1, and hos2 deletion mutants displayed similar defects as those observed in the tig1 mutant, but deletion of HST1 or HOS4 had no detectable phenotypes. Deletion of any of these core components of the Tig1 complex resulted in a significant reduction in HDAC activities. Our results showed that TIG1, like its putative yeast and mammalian orthologs, is one component of a conserved HDAC complex that is required for infectious growth and conidiogenesis in M. oryzae and highlighted that chromatin modification is an essential regulatory mechanism during plant infection.
Perception Optimized Deep Denoising AutoEncoders for Speech Enhancement

Speech Enhancement is a challenging and important area of research due to the many applications that depend on improved signal quality. It is a pre-processing step of speech processing systems and used for perceptually improving quality of speech for humans. With recent advances in Deep Neural Networks (DNN), deep Denoising Auto-Encoders have proved to be very successful for speech enhancement. In this paper, we propose a novel objective loss function, which takes into account the perceptual quality of speech. We use that to train PerceptuallyOptimized Speech Denoising Auto-Encoders (POS-DAE). We demonstrate the effectiveness of POS-DAE in a speech enhancement task. Further we introduce a two level DNN architecture for denoising and enhancement. We show the effectiveness of the proposed methods for a high noise subset of the QUT-NOISE-TIMIT database under mismatched noise conditions. Experiments are conducted comparing the POS-DAE against the Mean Square Error loss function using speech distortion, noise reduction and Perceptual Evaluation of Speech Quality. We find that the proposed loss function and the new 2stage architecture give significant improvements in perceptual speech quality measures and the improvements become more significant for higher noise conditions.
Regulation of gap junction channels by infectious agents and inflammation in the CNS

Gap junctions (GJs) are conglomerates of intercellular channels that connect the cytoplasm of two or more cells, and facilitate the transfer of ions and small molecules, including second messengers, resulting in metabolic and electrical coordination. In general, loss of gap junctional communication (GJC) has been associated with cellular damage and inflammation resulting in compromise of physiological functions. Recently, it has become evident that GJ channels also play a critical role in the pathogenesis of infectious diseases and associated inflammation. Several pathogens use the transfer of intracellular signals through GJ channels to spread infection and toxic signals that amplify inflammation to neighboring cells. Thus, identification of the mechanisms by which several infectious agents alter GJC could result in new potential therapeutic approaches to reduce inflammation and their pathogenesis.
EEG Signal Classification: Introduction to the Problem

The contribution describes the design, optimiza- tion and verification of the off-line single-trial movement classification system. Four types of movements are used for the classification: the right index finger extension vs. fle- xion as well as the right shoulder (proximal) vs. right index finger (distal) movement. The classification system utilizes hidden information stored in the characteristic shapes of human brain activity (EEG signal). The great variability of EEG potentials requires using of context information and hence the classifier based on Hidden Markov Models (HMM). The suitable parameterization, model structure as well as training and classification process are suggested on the base of spectral analysis results and experience with the speech recognition. The training and the classification are performed with the disjoint sets of EEG realizations. Classification experiments are performed with 10 random- ly chosen sets of EEG realizations. The final average score of the distal/proximal movement classification is 80%; the standard deviation of classifica- tion results is 9%. The classification of the extension / fle- xion gives comparable results.
Diode-pumped laser with Yb:YAG single-crystal fiber grown by the micro-pulling down technique

Recent developments of the micro-pulling down technique lead to efficient laser demonstration with Nd:YAG single crystal fibers. Indeed these media which benefit from the spectroscopic and thermal properties of bulk crystals and from the thin and long shape of glass fibers are ideal candidates for high average and high peak power laser systems. In this work, we investigate the potential of Yb:YAG single crystal fibers. After a careful design taking into account the quasithree level structure of the Yb3+ ions, we grew single crystal fibers by the micro-pulling down technique. With a 1 at. % doped and 40 mm long single crystal fiber of 1 mm in diameter, we obtained a power of 50 W in CW operation under 200 W of incident pump power. In the Q-switched regime, we achieved pulses with an energy of 1.8 mJ at 5 kHz and a duration of 13 ns for 120 W of pump power. We measured a M² value below 2.5. We also investigated the thermal management of our system by the use of thermal cartography and Finite Element Analysis, showing a maximum temperature smaller than 120°C reached on the pumped end face for 200 W of pump power. These results are a very promising to design high average power and high peak power laser sources.
Small-x dipole evolution beyond the large-N-c limit

We present a method to include colour-suppressed effects in the Mueller dipole picture. The model consistently includes saturation effects both in the evolution of dipoles and in the interactions of dipoles with a target in a frame-independent way. When implemented in a Monte Carlo simulation together with our previous model of energy-momentum conservation and a simple dipole description of initial state protons and virtual photons, the model is able to reproduce to a satisfactory degree both the gamma*p cross sections as measured at HERA as well as the total pp cross section all the way from ISR energies to the Tevatron and beyond.