Showing papers by "Université de Sherbrooke published in 2012"

Practical Bayesian Optimization of Machine Learning Algorithms

Abstract: The use of machine learning algorithms frequently involves careful tuning of learning parameters and model hyperparameters. Unfortunately, this tuning is often a "black art" requiring expert experience, rules of thumb, or sometimes brute-force search. There is therefore great appeal for automatic approaches that can optimize the performance of any given learning algorithm to the problem at hand. In this work, we consider this problem through the framework of Bayesian optimization, in which a learning algorithm's generalization performance is modeled as a sample from a Gaussian process (GP). We show that certain choices for the nature of the GP, such as the type of kernel and the treatment of its hyperparameters, can play a crucial role in obtaining a good optimizer that can achieve expertlevel performance. We describe new algorithms that take into account the variable cost (duration) of learning algorithm experiments and that can leverage the presence of multiple cores for parallel experimentation. We show that these proposed algorithms improve on previous automatic procedures and can reach or surpass human expert-level optimization for many algorithms including latent Dirichlet allocation, structured SVMs and convolutional neural networks.

Practical Bayesian Optimization of Machine Learning Algorithms

Abstract: Machine learning algorithms frequently require careful tuning of model hyperparameters, regularization terms, and optimization parameters. Unfortunately, this tuning is often a "black art" that requires expert experience, unwritten rules of thumb, or sometimes brute-force search. Much more appealing is the idea of developing automatic approaches which can optimize the performance of a given learning algorithm to the task at hand. In this work, we consider the automatic tuning problem within the framework of Bayesian optimization, in which a learning algorithm's generalization performance is modeled as a sample from a Gaussian process (GP). The tractable posterior distribution induced by the GP leads to efficient use of the information gathered by previous experiments, enabling optimal choices about what parameters to try next. Here we show how the effects of the Gaussian process prior and the associated inference procedure can have a large impact on the success or failure of Bayesian optimization. We show that thoughtful choices can lead to results that exceed expert-level performance in tuning machine learning algorithms. We also describe new algorithms that take into account the variable cost (duration) of learning experiments and that can leverage the presence of multiple cores for parallel experimentation. We show that these proposed algorithms improve on previous automatic procedures and can reach or surpass human expert-level optimization on a diverse set of contemporary algorithms including latent Dirichlet allocation, structured SVMs and convolutional neural networks.

A Systematic Review of Prevalence Studies on Multimorbidity: Toward a More Uniform Methodology

Abstract: PURPOSE We sought to identify and compare studies reporting the prevalence of multimorbidity and to suggest methodologic aspects to be considered in the conduct of such studies. METHODS We searched the literature for English- and French-language articles published between 1980 and September 2010 that described the prevalence of multimorbidity in the general population, in primary care, or both. We assessed quality of included studies with a modified version of the Strengthening the Reporting of Observational Studies in Epidemiology checklist. Results of individual prevalence studies were adjusted so that they could be compared graphically. RESULTS The final sample included 21 articles: 8 described studies conducted in primary care, 12 in the general population, and 1 in both. All articles were of good quality. The largest differences in prevalence of multimorbidity were observed at age 75 in both primary care (with prevalence ranging from 3.5% to 98.5% across studies) and the general population (with prevalence ranging from 13.1% to 71.8% across studies). Apart from differences in geographic settings, we identified differences in recruitment method and sample size (primary care: 980–60,857 patients; general population: 1,099–316,928 individuals), data collection, and the operational definition of multimorbidity used, including the number of diagnoses considered (primary care: 5 to all; general population: 7 to all). This last aspect seemed to be the most important factor in estimating prevalence. CONCLUSIONS Marked variation exists among studies of the prevalence of multimorbidity with respect to both methodology and findings. When undertaking such studies, investigators should carefully consider the specific diagnoses included and their number, as well as the operational definition of multimorbidity.

Changedetection.net: A new change detection benchmark dataset

Abstract: Change detection is one of the most commonly encountered low-level tasks in computer vision and video processing. A plethora of algorithms have been developed to date, yet no widely accepted, realistic, large-scale video dataset exists for benchmarking different methods. Presented here is a unique change detection benchmark dataset consisting of nearly 90,000 frames in 31 video sequences representing 6 categories selected to cover a wide range of challenges in 2 modalities (color and thermal IR). A distinguishing characteristic of this dataset is that each frame is meticulously annotated for ground-truth foreground, background, and shadow area boundaries — an effort that goes much beyond a simple binary label denoting the presence of change. This enables objective and precise quantitative comparison and ranking of change detection algorithms. This paper presents and discusses various aspects of the new dataset, quantitative performance metrics used, and comparative results for over a dozen previous and new change detection algorithms. The dataset, evaluation tools, and algorithm rankings are available to the public on a website1 and will be updated with feedback from academia and industry in the future.

Managing patients with multimorbidity: systematic review of interventions in primary care and community settings.

Abstract: Objective To determine the effectiveness of interventions designed to improve outcomes in patients with multimorbidity in primary care and community settings. Design Systematic review. Data sources Medline, Embase, CINAHL, CAB Health, Cochrane central register of controlled trials, the database of abstracts of reviews of effectiveness, and the Cochrane EPOC (effective practice and organisation of care) register (searches updated in April 2011). Eligibility criteria Randomised controlled trials, controlled clinical trials, controlled before and after studies, and interrupted time series analyses reporting on interventions to improve outcomes for people with multimorbidity in primary care and community settings. Multimorbidity was defined as two or more chronic conditions in the same individual. Outcomes included any validated measure of physical or mental health and psychosocial status, including quality of life outcomes, wellbeing, and measures of disability or functional status. Also included were measures of patient and provider behaviour, including drug adherence, utilisation of health services, acceptability of services, and costs. Data selection Two reviewers independently assessed studies for eligibility, extracted data, and assessed study quality. As meta-analysis of results was not possible owing to heterogeneity in participants and interventions, a narrative synthesis of the results from the included studies was carried out. Results 10 studies examining a range of complex interventions totalling 3407 patients with multimorbidity were identified. All were randomised controlled trials with a low risk of bias. Two studies described interventions for patients with specific comorbidities. The remaining eight studies focused on multimorbidity, generally in older patients. Consideration of the impact of socioeconomic deprivation was minimal. All studies involved complex interventions with multiple components. In six of the 10 studies the predominant component was a change to the organisation of care delivery, usually through case management or enhanced multidisciplinary team work. In the remaining four studies, intervention components were predominantly patient oriented. Overall the results were mixed, with a trend towards improved prescribing and drug adherence. The results indicated that it is difficult to improve outcomes in this population but that interventions focusing on particular risk factors in comorbid conditions or functional difficulties in multimorbidity may be more effective. No economic analyses were included, although the improvements in prescribing and risk factor management in some studies could provide potentially important cost savings. Conclusions Evidence on the care of patients with multimorbidity is limited, despite the prevalence of multimorbidity and its impact on patients and healthcare systems. Interventions to date have had mixed effects, although are likely to be more effective if targeted at risk factors or specific functional difficulties. A need exists to clearly identify patients with multimorbidity and to develop cost effective and specifically targeted interventions that can improve health outcomes.

A systematic literature review of 10 years of research on sex/gender and experimental pain perception - part 1: are there really differences between women and men?

Abstract: The purpose of this systematic review was to summarize and critically appraise the results of 10 years of human laboratory research on pain and sex/gender. An electronic search strategy was designed by a medical librarian and conducted in multiple databases. A total of 172 articles published between 1998 and 2008 were retrieved, analyzed, and synthesized. The first set of results (122 articles), which is presented in this paper, examined sex difference in the perception of laboratory-induced thermal, pressure, ischemic, muscle, electrical, chemical, and visceral pain in healthy subjects. This review suggests that females (F) and males (M) have comparable thresholds for cold and ischemic pain, while pressure pain thresholds are lower in F than M. There is strong evidence that F tolerate less thermal (heat, cold) and pressure pain than M but it is not the case for tolerance to ischemic pain, which is comparable in both sexes. The majority of the studies that measured pain intensity and unpleasantness showed no sex difference in many pain modalities. In summary, 10 years of laboratory research have not been successful in producing a clear and consistent pattern of sex differences in human pain sensitivity, even with the use of deep, tonic, long-lasting stimuli, which are known to better mimic clinical pain. Whether laboratory studies in healthy subjects are the best paradigm to investigate sex differences in pain perception is open to question and should be discussed with a view to enhancing the clinical relevance of these experiments and developing new research avenues.

Prediction of haematoma growth and outcome in patients with intracerebral haemorrhage using the CT-angiography spot sign (PREDICT): a prospective observational study.

Abstract: Summary Background In patients with intracerebral haemorrhage (ICH), early haemorrhage expansion affects clinical outcome. Haemostatic treatment reduces haematoma expansion, but fails to improve clinical outcomes in many patients. Proper selection of patients at high risk for haematoma expansion seems crucial to improve outcomes. In this study, we aimed to prospectively validate the CT-angiography (CTA) spot sign for prediction of haematoma expansion. Methods PREDICT (predicting haematoma growth and outcome in intracerebral haemorrhage using contrast bolus CT) was a multicentre prospective observational cohort study. We recruited patients aged 18 years or older, with ICH smaller than 100 mL, and presenting at less than 6 h from symptom onset. Using two independent core laboratories, one neuroradiologist determined CTA spot-sign status, whereas another neurologist masked for clinical outcomes and imaging measured haematoma volumes by computerised planimetry. The primary outcome was haematoma expansion defined as absolute growth greater than 6 mL or a relative growth of more than 33% from initial CT to follow-up CT. We reported data using standard descriptive statistics stratified by the CTA spot sign. Mortality was assessed with Kaplan-Meier survival analysis. Findings We enrolled 268 patients. Median time from symptom onset to baseline CT was 135 min (range 22–470), and time from onset to CTA was 159 min (32–475). 81 (30%) patients were spot-sign positive. The primary analysis included 228 patients, who had a follow-up CT before surgery or death. Median baseline ICH volume was 19·9 mL (1·5–80·9) in spot-sign-positive patients versus 10·0 mL (0·1–102·7) in spot-sign negative patients (p Interpretation These findings confirm previous single-centre studies showing that the CTA spot sign is a predictor of haematoma expansion. The spot sign is recommended as an entry criterion for future trials of haemostatic therapy in patients with acute ICH. Funding Canadian Stroke Consortium and NovoNordisk Canada.

Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities

Abstract: The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape-scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community-weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial-dominated microbial communities were associated with exploitative plant traits versus fungal-dominated communities with resource-conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.

Light-Responsive Block Copolymer Micelles

Abstract: The association state of light-responsive block copolymer (BCP) micelles in aqueous solution can be altered, often reversibly, by light. Driven by the potential application in controlled drug delivery, this type of stimuli-responsive polymer micelles has received increasing attention. This Perspective highlights the progress achieved in recent years. On the one hand, we discuss the different approaches of rational BCP design, making use of various photochromic moieties and photochemical reactions, and the underlying mechanisms leading to photoinduced disruption of BCP micelles. On the other hand, we suggest possible future directions in this area, including exploration of new mechanisms and chemistry and solutions to the excitation wavelength problem crucial for biomedical applications.

Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits: A Multi-Ethnic Meta-Analysis of 45,891 Individuals

Abstract: Circulating levels of adiponectin, a hormone produced predominantly by adipocytes, are highly heritable and are inversely associated with type 2 diabetes mellitus (T2D) and other metabolic traits. We conducted a meta-analysis of genome-wide association studies in 39,883 individuals of European ancestry to identify genes associated with metabolic disease. We identified 8 novel loci associated with adiponectin levels and confirmed 2 previously reported loci (P = 4.5×10(-8)-1.2×10(-43)). Using a novel method to combine data across ethnicities (N = 4,232 African Americans, N = 1,776 Asians, and N = 29,347 Europeans), we identified two additional novel loci. Expression analyses of 436 human adipocyte samples revealed that mRNA levels of 18 genes at candidate regions were associated with adiponectin concentrations after accounting for multiple testing (p<3×10(-4)). We next developed a multi-SNP genotypic risk score to test the association of adiponectin decreasing risk alleles on metabolic traits and diseases using consortia-level meta-analytic data. This risk score was associated with increased risk of T2D (p = 4.3×10(-3), n = 22,044), increased triglycerides (p = 2.6×10(-14), n = 93,440), increased waist-to-hip ratio (p = 1.8×10(-5), n = 77,167), increased glucose two hours post oral glucose tolerance testing (p = 4.4×10(-3), n = 15,234), increased fasting insulin (p = 0.015, n = 48,238), but with lower in HDL-cholesterol concentrations (p = 4.5×10(-13), n = 96,748) and decreased BMI (p = 1.4×10(-4), n = 121,335). These findings identify novel genetic determinants of adiponectin levels, which, taken together, influence risk of T2D and markers of insulin resistance.

Poly(vinyl alcohol) Hydrogel Can Autonomously Self-Heal

Abstract: It is discovered that poly(vinyl alcohol) (PVA) hydrogel prepared using the freezing/thawing method can self-repair at room temperature without the need for any stimulus or healing agent. The autonomous self-healing process can be fast for mechanically strong PVA hydrogel yielding a high fracture stress. Investigation on the effect of the hydrogel preparation conditions points out that hydrogen bonding between PVA chains across the interface of the cut surfaces is at the origin of the phenomenon. The key for an effective self-healing is to have an appropriate balance between high concentration of free hydroxyl groups on PVA chains on the cut surfaces prior to contact and sufficient PVA chain mobility in the hydrogel.

Near Infrared Light Triggered Release of Biomacromolecules from Hydrogels Loaded with Upconversion Nanoparticles

Abstract: Using a photosensitive hybrid hydrogel loaded with upconversion nanoparticles (UCNPs), we show that continuous-wave near-infrared (NIR) light (980 nm) can be used to induce the gel–sol transition and release large, inactive biomacromolecules (protein and enzyme) entrapped in the hydrogel into aqueous solution “on demand”, where their bioactivity is recovered. This study is a new demonstration and development in harnessing the unique multiphoton effect of UCNPs for photosensitive materials of biomedical interest.

A systematic literature review of 10 years of research on sex/gender and pain perception – Part 2: Do biopsychosocial factors alter pain sensitivity differently in women and men?

Abstract: This systematic review summarizes the results of 10 years of laboratory research on pain and sex/gender. An electronic search strategy was designed by a medical librarian to access multiple databases. A total of 172 articles published between 1998 and 2008 were retrieved, analyzed, and synthesized. The second set of results presented in this review (129 articles) examined various biopsychosocial factors that may contribute to differences in pain sensitivity between healthy women and men. The results revealed that the involvement of hormonal and physiological factors is either inconsistent or absent. Some studies suggest that temporal summation, allodynia, and secondary hyperalgesia may be more pronounced in women than in men. The evidence to support less efficient endogenous pain inhibitory systems in women is mixed and does not necessarily apply to all pain modalities. With regard to psychological factors, depression may not mediate sex differences in pain perception, while the role of anxiety is ambiguous. Cognitive and social factors appear to partly explain some sex-related differences. Finally, past individual history may be influential in female pain responses. However, these conclusions must be treated with much circumspection for various methodological reasons. Furthermore, some factors/mechanisms remain understudied in the field. There is also a need to assess and improve the ecological validity of findings from laboratory studies on healthy subjects, and perhaps a change of paradigm needs to be considered at this point in time to better understand the factors that influence the experience of women and men who suffer from acute or chronic pain.

Dipole coupling of a double quantum dot to a microwave resonator.

Abstract: We demonstrate the realization of a hybrid solid-state quantum device, in which a semiconductor double quantum dot is dipole coupled to the microwave field of a superconducting coplanar waveguide resonator. The double dot charge stability diagram extracted from measurements of the amplitude and phase of a microwave tone transmitted through the resonator is in good agreement with that obtained from transport measurements. Both the observed frequency shift and linewidth broadening of the resonator are explained considering the double dot as a charge qubit coupled with a strength of several tens of MHz to the resonator.

Community assembly along a soil depth gradient: contrasting patterns of plant trait convergence and divergence in a Mediterranean rangeland

Abstract: Summary 1. Understanding how environmental factors drive plant community assembly remains a major challenge in community ecology. The strength of different assembly processes along environmental gradients, such as environmental filtering and functional niche differentiation, can be quantified by analysing trait distributions in communities. While environmental filtering affects species occurrence among communities, functional divergence or convergence is strongly related to species abundances within communities, which few studies have taken into account. We examine the trait-mediated effect of these two processes along a stress-resource gradient. 2. We measured species abundances and the distributions of eight traits related to vegetative and regenerative phases in plant communities along a gradient of soil depth and resource availability in Mediterranean rangelands. We quantified environmental filtering, defined as a local restriction of trait range, and trait divergence, based on abundance-weighted trait variance, using a two-step approach with specifically designed null models. 3. Communities presented a clear functional response to the soil gradient, as evidenced by strong trends in community-weighted trait means. We detected environmental filtering of different traits at both ends of the gradient, suggesting that, contrary to widespread expectations, trait filtering may not necessarily be the result of abiotic filtering under harsh conditions but could likely also result from biotic interactions in productive habitats. 4. We found marked shifts in trait abundance distributions within communities along the gradient. Vegetative traits (e.g. leaf dry matter content) diverged on shallow soils, reflecting the coexistence of distinct water- and nutrient-use strategies in these constrained habitats and converged with increasing soil resource availability. By contrast, regenerative traits (e.g. seed mass) tended to diverge towards deeper soils, while plant reproductive heights diverged all along the gradient. 5. Synthesis: Our study highlights how the combination of abundance data with traits capturing different functional niches is critical to the detection of complex functional responses of plant communities to environmental gradients. We demonstrate that patterns of trait divergence and filtering are strongly contingent on both trait and environment such that there can be no expectation of a simple trend of increasing or decreasing functional divergence along a gradient of resource availability.

Implementation of a Toffoli gate with superconducting circuits

Abstract: Use of a three-level system allows the Toffoli gate, an important primitive for quantum error correction schemes, to be implemented with many fewer elementary gates than was previously thought possible. Quantum processors based on fragile quantum coherence are especially prone to errors due to sources of disturbance inevitable in any real system. The Toffoli gate, a logic gate that makes universal reversible classical computation possible, is a key element of universal quantum computation and error-correction schemes. Its realization is challenging, requiring many single and two-qubit operations executed with high fidelity. Fedorov et al. have developed a Toffoli gate in a superconducting circuit, exploiting three-level qubits to simplify implementation. Its performance confirms the potential of macroscopic superconducting qubits in complex quantum operations. The Toffoli gate is a three-quantum-bit (three-qubit) operation that inverts the state of a target qubit conditioned on the state of two control qubits. It makes universal reversible classical computation1 possible and, together with a Hadamard gate2, forms a universal set of gates in quantum computation. It is also a key element in quantum error correction schemes3,4,5,6,7. The Toffoli gate has been implemented in nuclear magnetic resonance3, linear optics8 and ion trap systems9. Experiments with superconducting qubits have also shown significant progress recently: two-qubit algorithms10 and two-qubit process tomography have been implemented11, three-qubit entangled states have been prepared12,13, first steps towards quantum teleportation have been taken14 and work on quantum computing architectures has been done15. Implementation of the Toffoli gate with only single- and two-qubit gates requires six controlled-NOT gates and ten single-qubit operations16, and has not been realized in any system owing to current limits on coherence. Here we implement a Toffoli gate with three superconducting transmon qubits coupled to a microwave resonator. By exploiting the third energy level of the transmon qubits, we have significantly reduced the number of elementary gates needed for the implementation of the Toffoli gate, relative to that required in theoretical proposals using only two-level systems. Using full process tomography and Monte Carlo process certification, we completely characterize the Toffoli gate acting on three independent qubits, measuring a fidelity of 68.5 ± 0.5 per cent. A similar approach15 to realizing characteristic features of a Toffoli-class gate has been demonstrated with two qubits and a resonator and achieved a limited characterization considering only the phase fidelity. Our results reinforce the potential of macroscopic superconducting qubits for the implementation of complex quantum operations with the possibility of quantum error correction17.

Everything You Ever Wanted to Know About Saccharomyces cerevisiae Telomeres: Beginning to End

Abstract: The mechanisms that maintain the stability of chromosome ends have broad impact on genome integrity in all eukaryotes. Budding yeast is a premier organism for telomere studies. Many fundamental concepts of telomere and telomerase function were first established in yeast and then extended to other organisms. We present a comprehensive review of yeast telomere biology that covers capping, replication, recombination, and transcription. We think of it as yeast telomeres—soup to nuts.

Eco-evolutionary responses of biodiversity to climate change

Abstract: explicit eco-evolutionary model of multi-species responses to climate change. We demonstrate that both dispersal and evolution differentially mediate extinction risks and biodiversity alterations through time and across climate gradients. Together, high genetic variance and low dispersal best minimized extinction risks. Surprisingly, high dispersal did not reduceextinctions,becausetheshiftingrangesofsomespecies hastened the decline of others. Evolutionary responses dominated during the later stages of climatic changes and in hot regions. No extinctions occurred without competition, which highlights the importance of including species interactions in global biodiversity models. Most notably, climate change createdextinctionandevolutionarydebts,withchangesinspecies richness and traits occurring long after climate stabilization. Therefore, even if we halt anthropogenic climate change today, transient eco-evolutionary dynamics would ensure centuries of additionalalterationsinglobalbiodiversity. Mostmodelsofspecies’responsestoclimatechangeexplorehow dispersal alone affects communities through shifting geographic ranges and ignore species interactions and evolutionary adaptation. However, species interactions often influence responses to climate 6 and climate-related traits can evolve rapidly 7,8 . Adaptation to new climates could moderate the direst predictions of biodiversity loss 9 whereas species interactions could enhance or diminish extinction risks depending on interaction type 10,11 . The available data do not yet permit the incorporation of these processes into quantitative estimates of extinction risk, but given the massive effort required to collect such data, a critical need exists for new theory to identify circumstances under which different processes may be particularly influential. Here we evaluate how ecological and evolutionary processes will interact in mediating species responses to climate change. To persist despite climate change, species need to disperse rapidly enough to track moving climate conditions, adapt to local conditions, or respond through plasticity 12 . These mechanisms interact with each other and with community dynamics through

Learning algorithms for the classification restricted Boltzmann machine

Abstract: Recent developments have demonstrated the capacity of restricted Boltzmann machines (RBM) to be powerful generative models, able to extract useful features from input data or construct deep artificial neural networks. In such settings, the RBM only yields a preprocessing or an initialization for some other model, instead of acting as a complete supervised model in its own right. In this paper, we argue that RBMs can provide a self-contained framework for developing competitive classifiers. We study the Classification RBM (ClassRBM), a variant on the RBM adapted to the classification setting. We study different strategies for training the ClassRBM and show that competitive classification performances can be reached when appropriately combining discriminative and generative training objectives. Since training according to the generative objective requires the computation of a generally intractable gradient, we also compare different approaches to estimating this gradient and address the issue of obtaining such a gradient for problems with very high dimensional inputs. Finally, we describe how to adapt the ClassRBM to two special cases of classification problems, namely semi-supervised and multitask learning.

Atmospheric Pressure Low Temperature Direct Plasma Technology: Status and Challenges for Thin Film Deposition

Abstract: Over the last ten years, expansion of atmospheric pressure plasma solutions for surface treatment of materials has been remarkable, however direct plasma technology for thin film deposition needs still great effort. The objective of this paper is to establish the state of the art on scientific and technologic locks, which have to be opened to consider direct atmospheric pressure plasma-enhanced chemical vapor deposition (AP-PECVD) a viable option for industrial application. Basic scientific principles to understand and optimize an AP-PECVD process are summarized. Laboratory reactor configurations are reviewed. Reference points for the design and use of AP-PECVD reactors according to the desired thin film properties are given. Finally, solutions to avoid powder formation and to increase the thin film growth rate are discussed.

Precursors of solvated electrons in radiobiological physics and chemistry.

Abstract: s; Proceeding of IX ECSBM, Prague, Czech Republic, 2001. (176) Abouaf, R.; Pommier, J.; Dunet, H. Int. J. Mass Spectrom. 2003, 226, 397. (177) Denifl, S.; Ptasin ́ska, S.; Cingel, M.; Matejcik, S.; Scheier, P.; Mar̈k, T. D. Chem. Phys. Lett. 2003, 377, 74. (178) Gohlke, S.; Abdoul-Carime, H.; Illenberger, E. Chem. Phys. Lett. 2003, 380, 595. (179) Abdoul-Carime, H.; Gohlke, S.; Illenberger, E. Phys. Rev. Lett. 2004, 92, 168103. (180) Ptasin ́ska, S.; Denifl, S.; Grill, V.; Mar̈k, T. D.; Scheier, P.; Gohlke, S.; Huels, M. A.; Illenberger, E. Angew. Chem., Int. Ed. 2005, 44, 1657. (181) Aflatooni, K.; Gallup, G. A.; Burrow, P. D. J. Phys. Chem. A 1998, 102, 6205. (182) Burrow, P. D.; Gallup, G. A.; Scheer, A. M.; Denifl, S.; Ptasinska, S.; Mar̈k, T. D.; Scheier, P. J. Chem. Phys. 2006, 124, 124310. (183) Aflatooni, K.; Scheer, A. M.; Burrow, P. D. Chem. Phys. Lett. 2005, 408, 426. (184) Naaman, R.; Sanche, L. Chem. Rev. 2007, 107, 1553. (185) Li, X.; Sevilla, M. D.; Sanche, L. J. Phys. Chem. B 2004, 108, 19013. (186) Ptasin ́ska, S.; Denifl, S.; Mroź, B.; Probst, M.; Grill, V.; Illenberger, E.; Scheier, P.; Mar̈k, T. D. J. Chem. Phys. 2005, 123, 124302. (187) Li, Z.; Cloutier, P.; Sanche, L.; Wagner, J. R. J. Phys. Chem. B 2011, 115, 13668. (188) Li, X.; Sevilla, M. D.; Sanche, L. J. Phys. Chem. B 2004, 108, 5472. (189) Ptasin ́ska, S.; Denifl, S.; Scheier, P.; Illenberger, E.; Mar̈k, T. D. Angew. Chem., Int. Ed. 2005, 44, 6941. (190) Zheng, Y.; Cloutier, P.; Hunting, D. J.; Wagner, J. R.; Sanche, L. J. Am. Chem. Soc. 2004, 126, 1002. (191) Huels, M. A.; Parenteau, L.; Michaud, M.; Sanche, L. Phys. Rev. A 1995, 51, 337. (192) Abdoul-Carime, H.; Cloutier, P.; Sanche, L. Radiat. Res. 2001, 155, 625. (193) Baccarelli, I.; Bald, I.; Gianturco, F. A.; Illenberger, E.; Kopyra, J. Phys. Rep. 2011, 508, 1. (194) Ptasin ́ska, S.; Denifl, S.; Scheier, P.; Mar̈k, T. D. J. Chem. Phys. 2004, 120, 8505. (195) Antic, D.; Parenteau, L.; Lepage, M.; Sanche, L. J. Phys. Chem. 1999, 103, 6611. (196) Antic, D.; Parenteau, L.; Sanche, L. J. Phys. Chem. B 2000, 104, 4711. (197) Huels, M. A.; Parenteau, L.; Sanche, L. J. Phys. Chem. B 2004, 108, 16303. (198) Pan, X.; Sanche, L. Chem. Phys. Lett. 2006, 421, 404. (199) Pan, X.; Sanche, L. Phys. Rev. Lett. 2005, 94, 198104. (200) Sulzer, P.; Mauracher, A.; Denifl, S.; Zappa, F.; Ptasin ́ska, S.; Beikircher, M.; Bacher, A.; Wendt, N.; Aleem, A.; Rondino, F.; Matejcik, S.; Probst, M.; Mar̈k, T. D.; Scheier, P. Anal. Chem. 2007, 79, 6585. (201) Gu, J.; Xie, Y.; Schaefer, H. F. Chem.Eur. J. 2010, 16, 5089. (202) Zheng, Y.; Cloutier, P.; Hunting, D. J.; Sanche, L.; Wagner, J. R. J. Am. Chem. Soc. 2005, 127, 16592. (203) Zheng, Y.; Wagner, J. R.; Sanche, L. Phys. Rev. Lett. 2006, 96, 208101. (204) Zheng, Y.; Cloutier, P.; Hunting, D. J.; Wagner, J. R.; Sanche, L. J. Chem. Phys. 2006, 124, 9. (205) Huels, M.; Boudaïffa, B.; Cloutier, P.; Hunting, D. J.; Sanche, L. J. Am. Chem. Soc. 2003, 125, 4467. (206) Boudaïffa, B.; Hunting, D. J.; Cloutier, P.; Huels, M. A.; Sanche, L. Int. J. Radiat. Biol. 2000, 76, 1209. (207) Boudaïffa, B.; Cloutier, P.; Hunting, D. J.; Huels, M. A.; Sanche, L. Med. Sci 2000, 16, 1281. (208) Martin, F.; Burrow, P. D.; Cai, Z.; Cloutier, P.; Hunting, D. J.; Sanche, L. Phys. Rev. Lett. 2004, 93, 068101. (209) Panajotovic, R.; Martin, F.; Cloutier, P.; Hunting, D. J.; Sanche, L. Radiat. Res. 2006, 165, 452. (210) Li, X.; Sevilla, M. D.; Sanche, L. J. Am. Chem. Soc. 2003, 125, 13668. (211) Simons, J. Acc. Chem. Res. 2006, 39, 772. (212) Bao, X.; Wang, J.; Gu, J.; Leszczynski, J. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 5658. (213) Caron, L.; Sanche, L. Phys. Rev. A: At., Mol. Opt. Phys. 2004, 70, 032719. (214) Caron, L. G.; Sanche, L. In Low-energy Electron Scattering from Molecules, Biomolecules and Surfaces; Čaŕsky, P., Čurík, R., Eds.; CRC Press (Taylor and Francis Group): Boca Raton, FL, 2012; pp 161− 230. (215) Lin, S. D. Radiat. Res. 1974, 59, 521. (216) Abdoul-Carime, H.; Sanche, L. Radiat. Res. 2003, 160, 86. (217) Abdoul-Carime, H.; Sanche, L. J. Phys. Chem. B 2004, 108, 457. (218) Abdoul-Carime, H.; Cecchini, S.; Sanche, L. Radiat. Res. 2002, 158, 23. (219) Ptasin ́ska, S.; Denifl, S.; Candor, P.; Matejcik, S.; Scheier, P.; Mar̈k, T. D. Chem. Phys. Lett. 2005, 403, 107. (220) Abdoul-Carime, H.; Gohlke, S.; Illenberger, E. Chem. Phys. Lett. 2005, 402, 497. (221) Gohlke, S.; Rosa, A.; Illenberger, E.; Brüning, F.; Huels, M. A. J. Chem. Phys. 2002, 116, 10164. (222) Ptasin ́ska, S.; Denifl, S.; Abedi, A.; Scheier, P.; Mar̈k, T. D. Anal. Bioanal. Chem. 2003, 377, 1115. (223) Abdoul-Carime, H.; Illenberger, E. Chem. Phys. Lett. 2004, 397, 309. (224) Sulzer, P.; Alizadeh, E.; Mauracher, A.; Scheier, P.; Mar̈k, T. D. Int. J. Mass. Spectrom. 2008, 277, 274. (225) Abdoul-Carime, H.; Gohlke, S.; Illenberger, E. Phys. Chem. Chem. Phys. 2004, 6, 161. (226) Alizadeh, E. Dissociative Electron Attachment to Biomolecules. Ph.D Thesis, University of Innsbruck, Innsbruck, Austria, August 2009. (227) Alizadeh, E.; Gschliesser, D.; Bartl, P.; Edtbauer, A.; Vizcaino, V.; Mauracher, A.; Probst, M.; Mar̈k, T. D.; Ptasin ́ska, S.; Mason, N. J.; Denifl, S.; Scheier, P. J. Chem. Phys. 2011, 134, 054305. (228) Vasil’ev, Y. V.; Figard, B. J.; Barofsky, D. F.; Deinzer, M. L. J. Am. Chem. Soc. 2007, 268, 106. (229) Cloutier, P.; Sicard-Roselli, C.; Escher, E.; Sanche, L. J. Phys. Chem. B 2007, 111, 1620. (230) Ptasin ́ska, S.; Li, Z.; Mason, N. J.; Sanche, L. Phys. Chem. Chem. Phys. 2010, 12, 9367. (231) Wang, J.; Gu, J.; Leszczynski, J. Chem. Phys. Lett. 2007, 442, 124. (232) Ptasin ́ska, S.; Sanche, L. Phys. Rev. E 2007, 75, 031915. (233) Falk, M.; Hartman, K. A.; Lord, R. C. J. Am. Chem. Soc. 1963, 85, 387. (234) Orlando, T. M.; Oh, D.; Chen, Y.; Aleksandrov, A. B. J. Chem. Phys. 2008, 128, 195102. (235) Dumont, A.; Zheng, Y.; Hunting, D.; Sanche, L. J. Chem. Phys. 2010, 132, 045102. (236) Solomun, T.; Skalicky, T. Chem. Phys. Lett. 2008, 453, 101. (237) Lett, J. T.; Alexander, P. Radiat. Res. 1961, 15, 159. Chemical Reviews Review dx.doi.org/10.1021/cr300063r | Chem. Rev. XXXX, XXX, XXX−XXX X (238) Neary, G. J.; Simpson-Gildemeister, V. F. W.; Peacocke, A. R. Int. J. Radiat. Biol. 1970, 18, 25. (239) Hearst, J. E.; Vinogard, J. Proc. Natl. Acad. Sci. U.S.A. 1961, 47, 825. (240) Saenger, W. Principles of Nucleic Acid Structure; SpringerVerlag: New York, NY, 1984. (241) Jeffrey, G.; Saenger, W. Hydration Bonding in Biological Structures; Springer-Verlag: New York, NY, 1991. (242) Tao, N. J.; Lindsay, S. M.; Rupprecht, A. Biopolymers 1989, 28, 1019. (243) Swarts, S.; Sevilla, M. D.; Becker, D.; Tokar, C.; Wheeler, K. Radiat. Res. 1992, 129, 333. (244) Brun, É.; Cloutier, P.; Sicard-Roselli, C.; Fromm, M.; Sanche, L. J. Phys. Chem. B 2009, 113, 10008. (245) Cai, Z.; Cloutier, P.; Hunting, D. J.; Sanche, L. J. Phys. Chem. B 2005, 109, 4796. (246) de Lara, C. M.; Jenner, T. J.; Townsend, K. M. S.; Marsden, S. J.; O’Neill, P. Radiat. Res. 1995, 144, 43. (247) Alizadeh, E.; Cloutier, P.; Hunting, D. J.; Sanche, L. J. Phys. Chem. B 2011, 115, 4796. (248) Samuni, A.; Czapski, G. Radiat. Res. 1978, 76, 624. (249) Roots, R.; Chatterjee, A.; Blakely, E.; Chang, P.; Smith, K.; Tobias, C. Radiat. Res. 1982, 92, 245. (250) Ewing, D.; Walton, H. L.; Guilfoil, D. S.; Ohm, M. B. Int. J. Radiat. Biol. 1991, 59, 717. (251) Alizadeh, E.; Sanche, L. Radiat. Phys. Chem. 2012, 81, 33. (252) Nikjoo, H.; Lindborg, L. Phys. Med. Biol. 2010, 55, R65. (253) Alizadeh, E.; Sanche, L. J. Phys. Chem. B 2011, 115, 14852. (254) Devita Jr, V. T.; Hellman, S.; Resenberg, S. A. Cancer: Principles and Practice of Oncology; Lippincott Williams and Wilkins: New York, NY, 2001. (255) Saif, M. W.; Diaso, R. B. In Chemoradiation in Cancer Therapy; Choy, H., Ed.; Humana Press: Totowa, NJ, 2003; pp 23−44. (256) Jamieson, E. R.; Lippard, S. J. Chem. Rev. 1999, 99, 2467. (257) Lippard, S. J. Pure Appl. Chem. 1987, 59, 731. (258) Zheng, Y.; Hunting, D. J.; Ayotte, P.; Sanche, L. Phys. Rev. Lett. 2008, 100, 198101. (259) Rezaee, M.; Hunting, D. J.; Sanche, L. Results to be published. (260) Rezaee, M.; Alizadeh, E.; Hunting, D. J.; Sanche, L. Bioinorg. Chem. Appl. 2011, 2012, 1. (261) Seiwert, T. Y.; Salama, J. K.; Vokes, E. E. Nat. Clin. Pract. Oncol. 2007, 4, 86. (262) Zimbrick, J. D.; Sukrochana, A.; Richmond, R. C. Int. J. Radiat. Oncol. Biol. Phys. 1979, 5, 1351. (263) Lelieveld, P.; Scoles, M. A.; Brown, J. M.; Kallman, R. F. Int. J. Radiat. Oncol. Biol. Phys. 1985, 11, 111. (264) Sanche, L. Chem. Phys. Lett. 2009, 474, 1 (and references therein). (265) Zheng, Y.; Hunting, D. J.; Ayotte, P.; Sanche, L. Radiat. Res. 2008, 169, 19. (266) Heb́ert, E. M.; debouttier̀e, P. J.; Lepage, M.; Sanche, L.; Hunting, D. J. Int. J. Radiat. Biol. 2010, 86, 692. (267) Herold, D. M.; Das, I. J.; Stobbe, C. C.; Iyer, R. V.; Chapman, J. D. Int. J. Radiat. Biol. 2000, 76, 1357. (268) Whyman, R. Gold Bull. 1996, 29, 11. (269) Chen, W.; Zhang, J. J. Nanosci. Nanotechnol. 2006, 6, 1159. (270) Anshup, A.; Venkataraman, J. S.; Subramaniam, C.; Kumar, R. R.; Priya, S.; Kumar, T. R. S.; Omkumar, R. V.; John, A.; Pradeep, T. Langmuir 2005, 21, 11562. (271) Niidome, T.; Nakashima, K.; Takahashi, H.; Niidome, Y. Chem. Commun. 2004, 17, 1978. (272) Brun, E.; Duchambon, P.; Blouquit, Y.; Keller, G.; Sanche, L.; Sicard-Roselli, C. Radiat. Phys. Chem. 2009, 78, 177. (273) Foley, E. A.; Carter, J. D.; Shan, F.; Guo, T. Chem. Commun. 2005, 25, 3192. (274) Carter, J. D.; Cheng, N. N.; Qu, Y.; Suarez, G. D.; Guo, T. J. Phys. Chem. B 2007, 111, 11622. (275) Butterworth, K. T.; Wyer, J. A.; Brennan-Fournet, M.; Latimer, C. J.; Shah, M. B.; Currell, F. J.; Hirst, D. G. Radiat. Res. 2008, 170, 381. (276) Chang, M.; Shiau, A.; Chen, Y.; Chang, C.; Chen, H.; Wu, C. Cancer Sci. 2008, 99, 1479. (277) Xiao, F.; Zheng, Z.; Cloutier, P.; He, Y.; Hunting, D. J.; Sanche, L. Nanotechnology 2011, 22, 465101. (278) Zheng, Y.; Sanche, L. Radiat. Res. 2009, 172, 114. (279) German, E. D.;

A Neural Autoregressive Topic Model

Abstract: We describe a new model for learning meaningful representations of text documents from an unlabeled collection of documents. This model is inspired by the recently proposed Replicated Softmax, an undirected graphical model of word counts that was shown to learn a better generative model and more meaningful document representations. Specifically, we take inspiration from the conditional mean-field recursive equations of the Replicated Softmax in order to define a neural network architecture that estimates the probability of observing a new word in a given document given the previously observed words. This paradigm also allows us to replace the expensive softmax distribution over words with a hierarchical distribution over paths in a binary tree of words. The end result is a model whose training complexity scales logarithmically with the vocabulary size instead of linearly as in the Replicated Softmax. Our experiments show that our model is competitive both as a generative model of documents and as a document representation learning algorithm.

General Strategy for Making CO2-Switchable Polymers

Abstract: By discovering that poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA) in water can react with carbon dioxide (CO2) and have its lower critical solution temperature (LCST) reversibly tuned by passing CO2 and argon (Ar) through the solution, we describe a general strategy for imparting a CO2-switchable LCST or water solubility to polymers of broad interest like poly(N-isopropylacrylamide) (PNIPAM) and poly[2-(2-methoxyethoxy)ethyl methacrylate] (PMEO2MA). We show that by easy copolymerization incorporating DMAEMA as a CO2-responsive trigger into PNIPAM or PMEO2MA, their LCST can effectively be switched by the gases. Two examples of applications were further demonstrated: upon CO2 or Ar bubbling at a constant solution temperature, hydrogels could undergo a reversible volume transition and block copolymer micelles could be dissociated and reassembled. This study opens the door to a wide range of easily accessible CO2-switchable polymers, enabling the use of CO2 as an effective trigger for smart materials an...

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Abstract: Mitogen-activated protein kinases (MAPKs) are evolutionarily conserved proteins that function as key signal transduction components in fungi, plants, and mammals. During interaction between phytopathogenic fungi and plants, fungal MAPKs help to promote mechanical and/or enzymatic penetration of host tissues, while plant MAPKs are required for activation of plant immunity. However, new insights suggest that MAPK cascades in both organisms do not operate independently but that they mutually contribute to a highly interconnected molecular dialogue between the plant and the fungus. As a result, some pathogenesis-related processes controlled by fungal MAPKs lead to the activation of plant signaling, including the recruitment of plant MAPK cascades. Conversely, plant MAPKs promote defense mechanisms that threaten the survival of fungal cells, leading to a stress response mediated in part by fungal MAPK cascades. In this review, we make use of the genomic data available following completion of whole-genome sequencing projects to analyze the structure of MAPK protein families in 24 fungal taxa, including both plant pathogens and mycorrhizal symbionts. Based on conserved patterns of sequence diversification, we also propose the adoption of a unified fungal MAPK nomenclature derived from that established for the model species Saccharomyces cerevisiae. Finally, we summarize current knowledge of the functions of MAPK cascades in phytopathogenic fungi and highlight the central role played by MAPK signaling during the molecular dialogue between plants and invading fungal pathogens.