Dataset for Automatic Summarization of Russian News

Automatic text summarization has been studied in a variety of domains and languages. However, this does not hold for the Russian language. To overcome this issue, we present Gazeta, the first dataset for summarization of Russian news. We describe the properties of this dataset and benchmark several extractive and abstractive models. We demonstrate that the dataset is a valid task for methods of text summarization for Russian. Additionally, we prove the pretrained mBART model to be useful for Russian text summarization.Comment: Version 3, accepted to AINL 202

Scientific discovery in a model-centric framework: Reproducibility, innovation, and epistemic diversity

Consistent confirmations obtained independently of each other lend credibility to a scientific result. We refer to results satisfying this consistency as reproducible and assume that reproducibility is a desirable property of scientific discovery. Yet seemingly science also progresses despite irreproducible results, indicating that the relationship between reproducibility and other desirable properties of scientific discovery is not well understood. These properties include early discovery of truth, persistence on truth once it is discovered, and time spent on truth in a long-term scientific inquiry. We build a mathematical model of scientific discovery that presents a viable framework to study its desirable properties including reproducibility. In this framework, we assume that scientists adopt a model-centric approach to discover the true model generating data in a stochastic process of scientific discovery. We analyze the properties of this process using Markov chain theory, Monte Carlo methods, and agent-based modeling. We show that the scientific process may not converge to truth even if scientific results are reproducible and that irreproducible results do not necessarily imply untrue results. The proportion of different research strategies represented in the scientific population, scientists' choice of methodology, the complexity of truth, and the strength of signal contribute to this counter-intuitive finding. Important insights include that innovative research speeds up the discovery of scientific truth by facilitating the exploration of model space and epistemic diversity optimizes across desirable properties of scientific discovery.Comment: EDITS: New title, corrected typos and errors, extended model and results descriptio

Reply to Comment by Jonathan J. Rhodes on ‘‘Modeling of the Interactions between Forest Vegetation, Disturbances, and Sediment Yields’’

Rhodes [2005] brings up some excellent points in his comments on the work of Istanbulluoglu et al. [2004]. We appreciate the opportunity to respond because it is likely that other readers will also wonder how they can apply the relatively simple analysis to important policy questions. Models necessarily reduce the complexity of the problem to make it tractable and synthesize some diverse sources of information. It may be helpful at times for readers to understand the high dimension of the complexity sacrificed in order to obtain the synthesis and the reasons for reducing the complexity in a particular manner. Rhodes [2005] comments on three things: (1) the omission of roads and landings from the analysis; (2) the implicit assumption that fire does not occur with harvesting; and (3) the overestimation of water repellency. We will respond to each of these, clarifying and elaborating on the basis for our modeling choices

Image Analysis for Cystic Fibrosis: Computer-Assisted Airway Wall and Vessel Measurements from Low-Dose, Limited Scan Lung CT Images

Cystic fibrosis (CF) is a life-limiting genetic disease that affects approximately 30,000 Americans. When compared to those of normal children, airways of infants and young children with CF have thicker walls and are more dilated in high-resolution computed tomographic (CT) imaging. In this study, we develop computer-assisted methods for assessment of airway and vessel dimensions from axial, limited scan CT lung images acquired at low pediatric radiation doses. Two methods (threshold- and model-based) were developed to automatically measure airway and vessel sizes for pairs identified by a user. These methods were evaluated on chest CT images from 16 pediatric patients (eight infants and eight children) with different stages of mild CF related lung disease. Results of threshold-based, corrected with regression analysis, and model-based approaches correlated well with both electronic caliper measurements made by experienced observers and spirometric measurements of lung function. While the model-based approach results correlated slightly better with the human measurements than those of the threshold method, a hybrid method, combining these two methods, resulted in the best results

Alemtuzumab pre-conditioning with tacrolimus monotherapy in pediatric renal transplantation

We employed antibody pre-conditioning with alemtuzumab and posttransplant immunosuppression with low-dose tacrolimus monotherapy in 26 consecutive pediatric kidney transplant recipients between January 2004 and December 2005. Mean recipient age was 10.7 ± 5.8 years, 7.7% were undergoing retransplantation, and 3.8% were sensitized, with a PRA >20%. Mean donor age was 32.8 ± 9.2 years. Living donors were utilized in 65% of the transplants. Mean cold ischemia time was 27.6 ± 6.4 h. The mean number of HLA mismatches was 3.3 ± 1.3. Mean follow-up was 25 ± 8 months. One and 2 year patient survival was 100% and 96%. One and 2 year graft survival was 96% and 88%. Mean serum creatinine was 1.1 ± 0.6 mg/dL, and calculated creatinine clearance was 82.3 ± 29.4 mL/min/1.73 m 2. The incidence of pre-weaning acute rejection was 11.5%; the incidence of delayed graft function was 7.7%. Eighteen (69%) of the children were tapered to spaced tacrolimus monotherapy, 10.5 ± 2.2 months after transplantation. The incidence of CMV, PTLD and BK virus was 0%; the incidence of posttransplant diabetes was 7.7%. Although more follow-up is clearly needed, antibody pre-conditioning with alemtuzumab and tacrolimus monotherapy may be a safe and effective regimen in pediatric renal transplantation. © 2007 The Authors

Evaluations of User-Driven Ontology Summarization

Ontology Summarization has been found useful to facilitate ontology engineering tasks in a number of different ways. Recently, it has been recognised as a means to facilitate ontology understanding and then support tasks like ontology reuse in ontology construction. Among the works in literature, not only distinctive methods are used to summarize ontology, also different measures are deployed to evaluate the summarization results. Without a set of common evaluation measures in place, it is not possible to compare the performance and therefore judge the effectiveness of those summarization methods. In this paper, we investigate the applicability of the evaluation measures from ontology evaluation and summary evaluation domain for ontology summary evaluation. Based on those measures, we evaluate the performances of the existing user-driven ontology summarization approaches

Screening of a Focused Ubiquitin-Proteasome Pathway Inhibitor Library Identifies Small Molecules as Novel Modulators of Botulinum Neurotoxin Type A Toxicity.

Botulinum neurotoxins (BoNTs) are known as the most potent bacterial toxins, which can cause potentially deadly disease botulism. BoNT Serotype A (BoNT/A) is the most studied serotype as it is responsible for most human botulism cases, and its formulations are extensively utilized in clinics for therapeutic and cosmetic applications. BoNT/A has the longest-lasting effect in neurons compared to other serotypes, and there has been high interest in understanding how BoNT/A manages to escape protein degradation machinery in neurons for months. Recent work demonstrated that an E3 ligase, HECTD2, leads to efficient ubiquitination of the BoNT/A Light Chain (A/LC); however, the dominant activity of a deubiquitinase (DUB), VCIP135, inhibits the degradation of the enzymatic component. Another DUB, USP9X, was also identified as a potential indirect contributor to A/LC degradation. In this study, we screened a focused ubiquitin-proteasome pathway inhibitor library, including VCIP135 and USP9X inhibitors, and identified ten potential lead compounds affecting BoNT/A mediated SNAP-25 cleavage in neurons in pre-intoxication conditions. We then tested the dose-dependent effects of the compounds and their potential toxic effects in cells. A subset of the lead compounds demonstrated efficacy on the stability and ubiquitination of A/LC in cells. Three of the compounds, WP1130 (degrasyn), PR-619, and Celastrol, further demonstrated efficacy against BoNT/A holotoxin in an in vitro post-intoxication model. Excitingly, PR-619 and WP1130 are known inhibitors of VCIP135 and USP9X, respectively. Modulation of BoNT turnover in cells by small molecules can potentially lead to the development of effective countermeasures against botulism

Role of bacteria in acute exacerbations of chronic obstructive pulmonary disease

Levent Erkan, Oguz Uzun, Serhat Findik, Didem Katar, Ahmet Sanic, Atilla G AticiOndokuz Mayis University, Faculty of Medicine, Department of Pulmonary Medicine, Samsun, TurkeyBackground and study objective: Infections are major causes of acute exacerbations of chronic obstructive pulmonary disease (COPD) which result in significant mortality and morbidity. The primary aim of the study was to determine the microbiological spectrum including atypical agents in acute exacerbations. The secondary aim was to evaluate resistance patterns in the microorganisms.Methods: The sputum culture of 75 patients admitted to our clinic from January 1, 1999 to December 31, 2002 was evaluated prospectively, for aerobic Gram-positive and Gram-negative bacteria, and serologically for Chlamydophila pneumoniae and Mycoplasma pneumoniae. Sensitivity patterns in potentially pathogenic microorganisms (PPMs) were also investigated.Results: An infectious agent was identified in 46 patients, either serologically or with sputum culture. Pathogens most commonly demonstrated were: Haemophilus influenzae (30%), Chlamydophila pneumoniae (17%), and Mycoplasma pneumoniae (9%). Mixed infections were diagnosed in 9 patients. PPMs showed a high resistance rate to commonly used antibiotics.Conclusion: We have shown that microorganisms causing acute exacerbations of COPD are not only typical bacteria (46%) but also atypical pathogens (26%), with unpredictable high rates. Typical agents showed a high resistance to commonly used antibiotics.Keywords: chronic obstructive pulmonary disease, acute exacerbation, infection, atypical pathogens, Haemophilus influenza