Miracle-dz/UniFAR-FTUs huggingface dataset:
Memory-efficient A* heuristics for multiple sequence alignment

The time and space needs of an A* search are strongly influenced by the quality of the heuristic evaluation function. Usually there is a trade-off since better heuristics may require more time and/or space to evaluate. Multiple sequence alignment is an important application for single-agent search. The traditional heuristic uses multiple pairwise alignments that require relatively little space. Three-way alignments produce better heuristics, but they are not used in practice due to the large space requirements. This paper presents a memory-efficient way to represent three-way heuristics as an octree. The required portions of the octree are computed on demand. The octree-supported three-way heuristics result in such a substantial reduction to the size of the A* open list that they offset the additional space and time requirements for the three-way alignments. The resulting multiple sequence alignments are both faster and use less memory than using A* with traditional pairwise heuristics.
Signal perception and transduction in plant defense responses.

Plant diseases have major effects on agricultural production and the food supply. Currently, worldwide crop losses due to disease are estimated to exceed $100 billion (Brears and Ryals 1994). Although application of fungicides and pestcides has helped control plant diseases, chemical control is economically costly as well as environmentally undesirable. Therefore, the development of new strategies based on a plant's own defense mechanisms for disease control is critical for sustaining agricultural production and improving our environment and health. Plant disease resistance and susceptibility are governed by the combined genotypes of host and pathogen and depend on a complex exchange of signals and responses occurring under given environmental conditions. During the long process of host-pathogen coevolution, plants have developed various elaborate mechanisms to ward off pathogen attack. Whereas some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection, others are induced only after pathogen attack. Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection. Recent studies have revealed intriguing parallels between animal and plant defense responses as demonstrated by the structural and functional conservation of some of their signal transduction processes. For example, several plant disease resistance (R) genes, which confer recognition and resistance to specific plant pathogens, were shown to encode an amino-terminal domain homologous to the cytoplasmic signaling domain of the mammalian interleukin-1 receptor and Drosophila Toll protein (Whitham et al. 1994; Lawrence et al. 1995; Anderson et al. 1997). The interleukin-1 receptor and Toll mediate cytokine-induced activation of NF-KB or Sp~itzle-induced activation of Dif/Dorsal, respectively, thereby leading to antimicrobial defense responses. In Drosophila, the genes spf~tzle, Toll, tube, pelle, and cactus are all re-
Learning Expressive Ontologies

The automatic extraction of ontologies from text and lexical resources has become more and more mature. Nowadays, the results of state-of-the-art ontology learning methods are already good enough for many practical applications. However, most of them aim at generating rather inexpressive ontologies, i.e. bare taxonomies and relationships, whereas many reasoning-based applications in domains such as bioinformatics or medicine rely on much more complex axiomatizations. Those are extremely expensive if built by purely manual efforts, and methods for the automatic or semi-automatic construction of expressive ontologies could help to overcome the knowledge acquisition bottleneck. At the same time, a tight integration with ontology evaluation and debugging approaches is required to reduce the amount of manual post-processing which becomes harder the more complex learned ontologies are. Particularly, the treatment of logical inconsistencies, mostly neglected by existing ontology learning frameworks, becomes a great challenge as soon as we start to learn huge and expressive axiomatizations. In this chapter we present several approaches for the automatic generation of expressive ontologies along with a detailed discussion of the key problems and challenges in learning complex OWL ontologies. We also suggest ways to handle different types of inconsistencies in learned ontologies, and conclude with a visionary outlook to future ontology learning and engineering environments.
Doubly robust inference for targeted minimum loss–based estimation in randomized trials with missing outcome data

Missing outcome data is a crucial threat to the validity of treatment effect estimates from randomized trials. The outcome distributions of participants with missing and observed data are often different, which increases bias. Causal inference methods may aid in reducing the bias and improving efficiency by incorporating baseline variables into the analysis. In particular, doubly robust estimators incorporate 2 nuisance parameters: the outcome regression and the missingness mechanism (ie, the probability of missingness conditional on treatment assignment and baseline variables), to adjust for differences in the observed and unobserved groups that can be explained by observed covariates. To consistently estimate the treatment effect, one of these nuisance parameters must be consistently estimated. Traditionally, nuisance parameters are estimated using parametric models, which often precludes consistency, particularly in moderate to high dimensions. Recent research on missing data has focused on data‐adaptive estimation to help achieve consistency, but the large sample properties of such methods are poorly understood. In this article, we discuss a doubly robust estimator that is consistent and asymptotically normal under data‐adaptive estimation of the nuisance parameters. We provide a formula for an asymptotically exact confidence interval under minimal assumptions. We show that our proposed estimator has smaller finite‐sample bias compared to standard doubly robust estimators. We present a simulation study demonstrating the enhanced performance of our estimators in terms of bias, efficiency, and coverage of the confidence intervals. We present the results of an illustrative example: a randomized, double‐blind phase 2/3 trial of antiretroviral therapy in HIV‐infected persons.
Biased Dismissal of Epigenetic Evidence for “Clean-Diesel” Carcinogenicity and Genotoxicity

In 2012, the International Agency for Research on Cancer (IARC) named Traditional Diesel Exhaust (TDE) a “known human carcinogen”. Most western nations agreed, passing new regulations. Yet the US denies TDE is a known carcinogen, says scientific data are uncertain, and does not regulate TDE emissions of 80 percent of US-diesel vehicles. It did require post-2007, US-heavy-duty-diesel vehicles to have “clean-diesel” or New-Technology-Diesel Exhaust (NTDE) --- filters/engine improvements to reduce emissions. A major reason the US disagrees with the rest of the world is its reliance on the 10-year series of US studies on NTDE, the 2015 Advanced Collaborative Emissions Study (ACES). Co-funded by US Environmental Protection Agency, ACES was overseen by the Health Effects Institute, a research group that the US National Academies of Science earlier praised. Who is right on diesel carcinogenicity, the hundreds of IARC, or the ACES, studies? This review article concludes IARC is correct. It (1) surveys the role of epigenetics in assessing TDE and NTDE carcinogenicity and genotoxicity. Next it (2) shows how, despite some ACES strengths, it ignored much epigenetic evidence for NTDE carcinogenicity and genotoxicity because of wrong/incomplete tests, trimming the data, using incorrect assessment-time frames, making value judgments instead of empirically-confirmed judgments, begging key questions---then invalidly concluding that NTDE causes “only a few mild effects on the lungs,” no cancer or serious ailments, and “no…gene- damaging effects. ” Finally the article (3) suggests why these scientific errors occurred in prominent studies and (4) answers objections to its criticisms of ACES.
Examining the Effectiveness of Solution-Focused Brief Therapy: A Meta-Analysis

Objective: A meta-analysis was conducted to evaluate the effectiveness of solution-focused brief therapy (SFBT). Method: Hierarchical linear modeling software was used to synthesize the primary studies to calculate an overall effect size estimate and test for between-study variability. Results: Solution-focused brief therapy demonstrated small but positive treatment effects favoring SFBT group on the outcome measures (d = 0.13 to 0.26). Only the magnitude of the effect for internalizing behavior problems was statistically significant at the p < . 05 level, thereby indicating that the treatment effect for SFBT group is different than the control group. Conclusions: This study allows social workers interested in solution-focused brief therapy to examine the empirical evidence quickly and with more definitive information.
Intraductal carcinoma of the prostate: the whole story

Summary Intraductal carcinoma of the prostate (IDC-P) is characterised by proliferation of malignant secretory cells that markedly expand prostatic ducts and acini. Its morphological features and diagnostic criteria have been refined in recent studies. Its molecular characteristics have also been increasingly elucidated. IDC-P is strongly associated with high grade and high volume invasive prostate cancer and unfavourable clinical outcomes. Therefore, it is critical to recognise and report IDC-P, especially in prostate biopsies where the clinical implications of the diagnosis are greatest. IDC-P has to be distinguished from several other prostate lesions with similar histological appearance. The distinction between IDC-P and high grade prostatic intraepithelial neoplasia is most important as they have drastically different implications for patient management. IDC-P is an uncommon finding in prostate biopsies, and is even rarer as an isolated finding without concomitant prostate cancer in biopsies. However, patients with isolated IDC-P in biopsies are recommended for either definitive treatment or immediate repeat biopsy. This article will review the historical aspect, diagnostic criteria, molecular genetics, and clinical significance of IDC-P.
Effectiveness analysis of using Solid State Disk technology

In the daily use of computer applications, large quantities of data are being written and read. Central Processing Unit, Random Access Memory and computer Hard Disk Drive are involved in that process. In 2008 / 2009 the massive commercial use of hard drives based on Solid State technology began, which are now rapidly replacing mechanical hard drives, made up of mechanical and electronic components (actuator, actuator arm, the motor that allows the rotation speed from 5400 rpm to 15000 rpm, controller, cache, etc.). Solid State Disk technology uses the same electronic interface as hard disk drives to communicate with the rest of the computer, which facilitates Solid State Disk installation and replacement of mechanical drives. Hard drives constructed in Solid State technology have the memory controller and flash memory on which the device performance primarily depends. Speed of writing and reading of data from the hard drive is extremely affecting the operation of the entire computer system, especially database search, the playback / recording of audio-video and daily data read / copy. The research described in this paper will compare the speed of writing / reading of the mechanical hard drive with the speed of writing / reading of the hard drive in SSD technology. The comparison will be conducted through synthetic tests with ATTO Disk Benchmark tool. Solid State Disk technology can also be viewed according to the "Green computing” concept, meaning reduced expenses (less energy consumption, less cooling costs for data centers, servers, PCs) and higher performance). Comparison results between these two technologies will provide a cost-effective argumentation in favor of switching to SSD technology.
INTRINSIC PALINDROMES

Natural numbers occur everywhere in our daily life: a bus ticket, a car plate, an id number, a timetable, etc. These numbers are mostly expressed in the decimal system. That is, for a natural numbers n ∈ N we write n = (ak−1 . . . a0)10 for some 0 ≤ ai ≤ 9 and ak−1 6= 0, which means that n = ak−110 + ak−210 + · · ·+ a0. Of particular interest are the so-called palindromic numbers. These are the numbers whose decimal expansion is the same when read from left to right, and from right to left, that is (ak−1 . . . a0)10 = (a0 . . . ak−1)10. This kind of number appears already in the Ganitasârasamgraha, a sanskrit manuscript dated around 850 AD. Therein the Indian mathematician Mahâv̂irâchârya described 12345654321 as the quantity which “beginning with one until it reaches six, then decreases in reverse order” [1, p. 399]. This is a curious palindromic number, and in particular it is the square of another palindrome: 12345654321 = 111111. There are many ways of generating palindromic numbers (see for instance [2]) including an interesting conjectural one [3]. Running across a palindrome by chance is a rare occurrence: for instance, the probability of picking at random a number 10 ≤ n < 10 and obtaining a palindrome is 1/10, a fact well-known by the collectors of palindromic bus tickets. Hence we tend to feel pretty lucky when one of these rare numbers crosses our path. And the more digits it has, the luckier we feel, and the luckier the number itself seems to be. But, is this feeling really justified? The truth has to be said: this property is not intrinsic to the number, but also depends on the base used to express it. So the number n := (894111498)10 is lucky (or palindromic) in base 10, but is not in base 13 as n = (113314377)13. Hence each time we encounter 894111498 we have to – at least in principle – thank heaven for this occurrence together with the fact that the human race has five fingers in each hand. However, we can easily get independent of the base by defining a number to be intrinsically palindromic if it is palindromic in some base. A little reflection shows that this definition is meaningless as it stands: every number is palindromic in any base m > n, as n = (n)m. Indeed it is much more natural to take into account the number of digits. So we define a number n ∈ N to be k-palindromic if there is a base b such that the b-expansion of n is palindromic of length k. The previous observation shows that every number if 1-palindromic. Also note that n = (11)n−1 provided that n ≥ 3, that is every n ≥ 3 is 2-palindromic. What about k-palindromic numbers for k ≥ 3? Our thesis is that very few numbers are k-palindromic, at least for k ≥ 4. The probability of a number in an appropriate range being,
Fairness and competence in citizen participation : evaluating models for environmental discourse

Foreword. Preface: Democracy and Science T. Dietz. 1. A Need for Discourse on Citizen Participation: Objectives and Structure of the Book O. Renn, T. Webler, P. Wiedemann. 2. A Brief Primer on Participation: Philosophy and Practice T. Webler, O. Renn. 3. 'Right' Discourse in Citizen Participation: An Evaluative Yardstick T. Webler. 4. The Redemption of Citizen Advisory Committees: A Perspective from Critical Theory F. M. Lynn, J. D. Kartez. 5. Citizens' Advisory Committee as a Model For Public Participation: A Multiple-Criteria Evaluation A. Vari. 6. Planning Cells: A Gate to 'Fractal' Mediation P. C. Dienel, O. Renn. 7. Review of 'Planning Cells': Problems of Legitimation H. -J. Seiler. 8. Citizens' Juries: One Solution for Difficult Environmental Questions N. Crosby. 9. The Citizens' Jury as Model of Public Participation: A Critical Evaluation A. Armour. 10. The Varresbecker Bach Participatory Process: The Model of Citizen Initiatives F. Claus. 11. The Varresbecker Bach Participatory Process: An Evaluation J. Linnerooth- Bayer. 12. Regulatory Negotiation as a Form of Public Participation D. Fiorino. 13. Regulatory Negotiation as Citizen Participation: A Critique S. G. Hadden. 14. Mediation M. Baughman. 15. Environmental Mediation: Insights into the Microcosm and Outlooks for Political Implications W. Nothdurft. 16. Voluntary Siting of Noxious Facilities: The Role of Compensation H. Kunreuther. 17. Voluntary Siting of Noxious Facilities: Additional Thoughts and Empirical Evidence F. Oberholzer-Gee, B. S. Frey. 18. Direct Participation in Macro-Issues: A Multiple Group Approach. An Analysis and Critique of the Dutch National Debate on Energy Policy, Fairness, Competence, and Beyond C. J. H. Midden. 19. The Dutch Study Groups Revisited J. L. Mumpower. 20. The Pursuit of Fair and Competent Citizen Participation O. Renn, T. Webler, P. Wiedemann. Appendix: Biographies of Authors. Index.
Neuroendocrine lung cancer: a receptor-mediated disease?

Neuroendocrine lung cancer is traditionally subclhssified into small cell cancer, atypical carcinoids, and carcinoids [1] . Among these, small cell cancer is one of the most common pulmonary neoplasms found in humans and occurs almost exclusively in~people who smoke [2]i A similar exposure-disease association has nor been esoabLished for the carcinoids, possibly because these rumors are relatively rare [1, 21 . Small cell cancer is an extremely aggressive rumor that tends to metastasize extensively at an early stage . Although~ an initial response to radiotherapy and chemotherapy is common, the rumors usually develop drug resistance and survival beyond 12 months of diagnosis is rare [3]. In contrast, carcinoids are generally slow-growing, more benign lesions with~only low-metastatic potential and a low-recurrence rate after surgical reseeZion [1, 3] . Despite their profound differences in clinical behavior, all~ three types of neuroendocrine lung rumors express one or several neuroendocrine markers . Among these, secretion of the peptides mammalian bombesin (1VIB) and calcitoni.n (CT) and expression of neuron specific enolase (NSE), [. -dopa decarboxylase, and electron-dense neuroendocrine secretion granules are the most common [3] . For decades, scientists have wondered why a type of rumor that demonstrates such convincing epidemiologic link with smoking seemed to be nonreproducible in animal' experimentations, all~ of'~ which attempted to mimic ex-
Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28

Streptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent. Indeed, sequence type (ST) 28 serotype 2 S. suis strains have been described as a homogeneous group of low virulence. However, ST28 strains are often isolated from diseased swine in some countries, and at least four human ST28 cases have been reported. Here, we used whole-genome sequencing and animal infection models to test the hypothesis that the ST28 lineage comprises strains of different genetic backgrounds and different virulence. We used 50 S. suis ST28 strains isolated in Canada, the United States and Japan from diseased pigs, and one ST28 strain from a human case isolated in Thailand. We report a complex population structure among the 51 ST28 strains. Diversity resulted from variable gene content, recombination events and numerous genome-wide polymorphisms not attributable to recombination. Phylogenetic analysis using core genome single-nucleotide polymorphisms revealed four discrete clades with strong geographic structure, and a fifth clade formed by US, Thai and Japanese strains. When tested in experimental animal models, strains from this latter clade were significantly more virulent than a Canadian ST28 reference strain, and a closely related Canadian strain. Our results highlight the limitations of MLST for both phylogenetic analysis and virulence prediction and raise concerns about the possible emergence of ST28 strains in human clinical cases.
A new Improved Round Robin-Based Scheduling Algorithm-A comparative Analysis

CPU or process Scheduling, which is an important part in any operating systems, allocates processes to the CPU in specific order to optimize some objective functions. The efficiency of any operating system relies strongly on the scheduling algorithms used. A number of scheduling algorithms exists. Among them, Round Robin (RR) is the most widely utilized algorithm. RR has proved to be effective in several types of operating systems, such as time sharing systems. This is due to the reasonable response time it gives. However, it suffers from some shortcomings such as high average turnaround time, high average waiting time as well as many context switches. Recently, several algorithms have been proposed to improve its efficiency, however, few studies were conducted to compare their efficiency when applied to dataset with different characteristics. The aim of this paper is three-fold: (1) presenting a survey of various RR based scheduling algorithms proposed and found in literature, (2) proposing a new RR based approach named, the Eighty-Five Percentile Round-Robin algorithm (EFPRR), to overcome the aforementioned issues, and (3) Conducting comparisons between eight RR based algorithms and the proposed approach using datasets with different characteristics. Extensive experiments have been done to test the proposed approach. Experimentally, the proposed approach has proven to perform better than other algorithms.
Structural Framework for Covalent Inhibition of Clostridium botulinum Neurotoxin A by Targeting Cys165*

Background: Development of small potent synthetic inhibitors of Clostridium botulinum neurotoxin A remains an unresolved challenge. Results: Small compounds incorporating electrophile moiety can block enzyme activity by covalent modification of Cys165. Conclusion: A structural framework for developing potent covalent inhibitors of Clostridium botulinum neurotoxin A is provided. Significance: This study uncovers a subfamily of zinc proteases containing a conserved cysteine in their active site. Clostridium botulinum neurotoxin type A (BoNT/A) is one of the most potent toxins for humans and a major biothreat agent. Despite intense chemical efforts over the past 10 years to develop inhibitors of its catalytic domain (catBoNT/A), highly potent and selective inhibitors are still lacking. Recently, small inhibitors were reported to covalently modify catBoNT/A by targeting Cys165, a residue located in the enzyme active site just above the catalytic zinc ion. However, no direct proof of Cys165 modification was reported, and the poor accessibility of this residue in the x-ray structure of catBoNT/A raises concerns about this proposal. To clarify this issue, the functional role of Cys165 was first assessed through a combination of site-directed mutagenesis and structural studies. These data suggested that Cys165 is more involved in enzyme catalysis rather than in structural property. Then by peptide mass fingerprinting and x-ray crystallography, we demonstrated that a small compound containing a sulfonyl group acts as inhibitor of catBoNT/A through covalent modification of Cys165. The crystal structure of this covalent complex offers a structural framework for developing more potent covalent inhibitors catBoNT/A. Other zinc metalloproteases can be founded in the protein database with a cysteine at a similar location, some expressed by major human pathogens; thus this work should find broader applications for developing covalent inhibitors.