Miracle-dz/UniFAR-FTUs huggingface dataset:
Using evolutionary Expectation Maximization to estimate indel rates

Abstract Motivation: The Expectation Maximization (EM) algorithm, in the form of the Baum–Welch algorithm (for hidden Markov models) or the Inside-Outside algorithm (for stochastic context-free grammars), is a powerful way to estimate the parameters of stochastic grammars for biological sequence analysis. To use this algorithm for multiple-sequence evolutionary modelling, it would be useful to apply the EM algorithm to estimate not only the probability parameters of the stochastic grammar, but also the instantaneous mutation rates of the underlying evolutionary model (to facilitate the development of stochastic grammars based on phylogenetic trees, also known as Statistical Alignment). Recently, we showed how to do this for the point substitution component of the evolutionary process; here, we extend these results to the indel process. Results: We present an algorithm for maximum-likelihood estimation of insertion and deletion rates from multiple sequence alignments, using EM, under the single-residue indel model owing to Thorne, Kishino and Felsenstein (the ‘TKF91’ model). The algorithm converges extremely rapidly, gives accurate results on simulated data that are an improvement over parsimonious estimates (which are shown to underestimate the true indel rate), and gives plausible results on experimental data (coronavirus envelope domains). Owing to the algorithm's close similarity to the Baum–Welch algorithm for training hidden Markov models, it can be used in an ‘unsupervised’ fashion to estimate rates for unaligned sequences, or estimate several sets of rates for sequences with heterogenous rates. Availability: Software implementing the algorithm and the benchmark is available under GPL from http://www.biowiki. org/ Contact: ihh@berkeley.edu
Simple Path Planning Algorithm for Two-Wheeled Differentially Driven (2WDD) Soccer Robots

Well designed path planning algorithms are the key factor for moving robots. This paper describes a novel simple approach based on kinematics. The testing bed is a tiny two-wheeled robot. The robot’s movement is specified by its translatoric velocity vR and its angular velocity ωR. The kinematic approach generates piecewise circular arcs based on a number of possible different sets of boundary conditions in the target positions.
Ribavirin Antagonizes the In Vitro Anti-Hepatitis C Virus Activity of 2′-C-Methylcytidine, the Active Component of Valopicitabine

ABSTRACT Ribavirin antagonizes the in vitro anti-hepatitis C virus (HCV) activity of the pyrimidine nucleoside analogue 2′-C-methylcytidine, the active component of the experimental anti-HCV drug valopicitabine. In contrast, the combination of ribavirin with either the purine nucleoside analogue 2′-C-methyladenosine or the HCV protease inhibitor VX-950 resulted in an additive antiviral activity. These findings may have implications when planning clinical studies with valopicitabine.
The Necessity for Hardware QoS Support for Server Consolidation and Cloud Computing

Chip multiprocessors (CMPs) are ubiquitous in most of today's computing fields. Although they provide noticeable benefits in terms of performance, cost and power efficiency, they also introduce some new issues. In this paper we analyze how the interference from Virtual Private Servers running in other cores is a significant component of performance unpredictability and can threaten the attainment of cloud computing. Even if virtualization is used, the sharing of the on-chip section of the memory hierarchy by different cores makes performance isolation strongly dependent on what is running elsewhere in the system. We will show in three actual computing systems, based on Sun UltraSparc T1, Sun UltraSparc T2 and Intel Xeon processors, how state-of-the-art virtualization techniques are unable to guarantee performance isolation in a representative workload such as SPECweb2005. In an especially conceived near worst-case scenario, it is possible to reduce the performance achieved by a Solaris Zones consolidated server for this suite of benchmarks in a Sun Fire T1000 and a Sun Enterprise T5120 by up to 80%. The performance drop observed by a Xen consolidated server running in a HP Proliant DL160 G5 is almost 45%. For all systems under study, off-chip bandwidth is shown to be the most critical resource.
Measuring Botnets in the Wild: Some New Trends

Today, botnets are still responsible for most large scale attacks on the Internet. Botnets are versatile, they remain the most powerful attack platform by constantly and continuously adopting new techniques and strategies in the arms race against various detection schemes. Thus, it is essential to understand the latest of the botnets in a timely manner so that the insights can be utilized in developing more efficient defenses. In this work, we conduct a measurement study on some of the most active botnets on the Internet based on a public dataset collected over a period of seven months by a monitoring entity. We first examine and compare the attacking capabilities of different families of today's active botnets. Our analysis clearly shows that different botnets start to collaborate when launching DDoS attacks.
Chromosomal damage in peripheral blood lymphocytes from nurses occupationally exposed to chemicals

In the present study, we evaluated the induced genome damage in peripheral blood lymphocytes from a sample of nurses occupationally exposed to low doses of different chemicals. A comprehensive multi-biomarker approach using cytogenetic endpoints was employed for analyzing chromosomal aberrations (CAs) and sister chromatid exchange (SCE) assay. The study included 20 nurses and 20 control subjects matched in age, gender and smoking habits. Nurses were exposed to different chemicals, such as cytostatic drugs, anaesthetics, formaldehyde and other sterilizing gases. Significant differences were found between exposure group and control group in terms of SCEs frequency (p < 0.001) but not in terms of replication index value (p = 0.845) and CAs (p = 0.236). Regression analyses indicated that the age and the exposure years did not influence the amount of the chromosomal damage among nurses. Vice versa, among controls, a positive correlation was found between the number of SCEs and age. In conclusion, our results suggest that a continuous long-term exposure to low doses of chemicals could result in increased levels of SCEs among nurses. This data emphasize the importance of biomonitoring nurses and other hospital workers handling drugs.
Dopaminergic Mechanisms in Actions and Habits

Recent studies suggest new ways to interpret dopaminergic actions in goal-directed performance and habitual responding. In the early stages of learning dopamine plays an essential role, but with extended training dopamine appears to play a decreasing role in response expression. Experimental manipulation of dopamine levels alters the correlation of cortical and striatal neural activity in behaving animals, and these dopamine-dependent changes in corticostriatal correlations may be reflected in changes in action selection in the basal ganglia. Consistent with this hypothesis, changes in dopamine signaling brought about by sensitization with amphetamine mimic the transition from goal-directed to habit-based instrumental performance. At the cellular level, dopamine-dependent synaptic plasticity may be important initially, and subsequently lead to more persistent changes that no longer require dopamine. The locus of these actions within the cortical and corticostriatal circuitry is a focus on ongoing research.
Chlamydia-Specific CD4 T Cell Clones Control Chlamydia muridarum Replication in Epithelial Cells by Nitric Oxide-Dependent and -Independent Mechanisms

Chlamydia trachomatis serovars D–K are sexually transmitted intracellular bacterial pathogens that replicate in epithelial cells lining the human reproductive tract. It is clear from knockout mice and T cell depletion studies using Chlamydia muridarum that MHC class II and CD4 T cells are critical for clearing bacteria from the murine genital tract. It is not clear how CD4 T cells interact with infected epithelial cells to mediate bacterial clearance in vivo. Previous work using an epithelial tumor cell line showed that a Chlamydia-specific CD4 T cell clone was able to inhibit C. muridarum replication in vitro via induction of epithelial NO production. We have previously shown that Chlamydia-specific CD4 T cell clones can recognize and be activated by infected reproductive tract epithelial cells and block Chlamydia replication in them. We extend those observations by investigating the mechanism used by a panel of CD4 T cell clones to control Chlamydia replication in epithelial cells. We found that Chlamydia-specific CD4 T cell clones were cytolytic, but that cytolysis was not likely critical for controlling C. muridarum replication. For one, CD4 T cell clone-induced epithelial NO production was critical for controlling replication; however, the most potent CD4 T cell clones were dependent on T cell degranulation for replication control with only a minor additional contribution from NO production. We discuss our data as they relate to existing knockout mouse studies addressing mechanisms of T cell-mediated control of Chlamydia replication and their implications for intracellular epithelial pathogens in mouse models.
The Synergistic Effect of Concomitant Schistosomiasis, Hookworm, and Trichuris Infections on Children's Anemia Burden

Objective To estimate the degree of synergism between helminth species in their combined effects on anemia. Methods Quantitative egg counts using the Kato–Katz method were determined for Ascaris lumbricoides, hookworm, Trichuris trichiura, and Schistosoma japonicum in 507 school-age children from helminth-endemic villages in The Philippines. Infection intensity was defined in three categories: uninfected, low, or moderate/high (M+). Anemia was defined as hemoglobin <11 g/dL. Logistic regression models were used to estimate odds ratios (OR), 95% confidence intervals (CI), and synergy index for pairs of concurrent infections. Results M+ co-infection of hookworm and S. japonicum (OR = 13.2, 95% CI: 3.82–45.5) and of hookworm and T. trichiura (OR = 5.34, 95% CI: 1.76–16.2) were associated with higher odds of anemia relative to children without respective M+ co-infections. For co-infections of hookworm and S. japonicum and of T. trichiura and hookworm, the estimated indices of synergy were 2.9 (95% CI: 1.1–4.6) and 1.4 (95% CI: 0.9–2.0), respectively. Conclusion Co-infections of hookworm and either S. japonicum or T. trichiura were associated with higher levels of anemia than would be expected if the effects of these species had only independent effects on anemia. This suggests that integrated anti-helminthic treatment programs with simultaneous deworming for S. japonicum and some geohelminths could yield a greater than additive benefit for reducing anemia in helminth-endemic regions.
Hybrid textbook: fusion of digital textbooks and traditional learning tools

In contemporary learning environments, tablet computers are often used to display digital textbooks; however, they are not expected to replace all traditional learning tools. Initially, we developed the paper-top interface PTI as a note-taking support system based on augmented-reality technology. The PTI is a fusion of digital textbooks and traditional learning tools. The PTI system projects a digital textbook onto a paper notebook using a pico projector and enables students to annotate the textbook using a pencil and an eraser. In the present study, we focused primarily on interactive quizzes in a digital textbook and extended the original PTI by diversifying interactions through various input operations. We performed comparative experiments to clarify the effectiveness of the PTI as note-taking support for a digital textbook. The experimental results show that the PTI is not inferior to other note-taking techniques and that the new interactions can increase learning motivation and effectiveness.
Design and Management of Voltage-Frequency Island Partitioned Networks-on-Chip

The design of many core systems-on-chip (SoCs) has become increasingly challenging due to high levels of integration, excessive energy consumption and clock distribution problems. To deal with these issues, we consider network-on-chip (NoC) architectures partitioned into several voltage-frequency islands (VFIs) and propose a design methodology for runtime energy management. The proposed approach minimizes the energy consumption subject to performance constraints. Then, we present efficient techniques for on-the-fly workload monitoring and management to ensure that the system can cope with variability in the workload and various technology-related parameters. Simulation results demonstrate the effectiveness of our approach in reducing the overall system energy consumption for a real video application. Finally, the results and functional correctness are validated using an field-programmable gate-array (FPGA) prototype for an NoC with multiple VFIs.
PLANT RESPONSES TO CLIMATE IN THE CAPE FLORISTIC REGION OF SOUTH AFRICA: EVIDENCE FOR ADAPTIVE DIFFERENTIATION IN THE PROTEACEAE

Local adaptation along environmental gradients may drive plant species radiation within the Cape Floristic Region (CFR), yet few studies examine the role of ecologically based divergent selection within CFR clades. In this study, we ask whether populations within the monophyletic white protea clade (Protea section Exsertae, Proteaceae) differ in key functional traits along environmental gradients and whether differences are consistent with local adaptation. Using seven taxa, we measured trait–environment associations and selection gradients across 35 populations of wild adults and their offspring grown in two common gardens. Focal traits were leaf size and shape, specific leaf area (SLA), stomatal density, growth, and photosynthetic rate. Analyses on wild and common garden plants revealed heritable trait differences that were associated with gradients in rainfall seasonality, drought stress, cold stress, and less frequently, soil fertility. Divergent selection between gardens generally matched trait–environment correlations and literature‐based predictions, yet variation in selection regimes among wild populations generally did not. Thus, selection via seedling survival may promote gradient‐wide differences in SLA and leaf area more than does selection via adult fecundity. By focusing on the traits, life stages, and environmental clines that drive divergent selection, our study uniquely demonstrates adaptive differentiation among plant populations in the CFR.
A survey of attitudes, beliefs, and perceptions regarding the internationalization of engineering and Computer Science undergraduate programs at the University of Victoria

Canadian undergraduate and graduate programs in Engineering and Computer Science attract a large number of international students. This is a relatively recent phenomenon with social and academic implications that are not completely understood. We are aware that more can be done for the recruitment, retention, and more generally for increasing the quality of the learning experience of our international students. More efforts need to be made in order to foster and expand social and academic interactions between Canadian and international students, as well as student-faculty interactions. The research described in this paper aims to identify the first steps in creating an inclusive environment that fosters academic, social, and personal growth for both international and Canadian students. This study discusses data collected about the experience of international undergraduate students in the Faculty of Engineering our university. The purpose of the data collection was to determine their specific needs, and to solicit suggestions and recommendations about ways in which to address them.
A comparator-based cyclic analog-to-digital converter with boosted preset voltage

In this paper, we describe a cyclic ADC to adopt the comparator-based switched-capacitor (CBSC) technique, for the first time, so as to compensate for the technology scaling and reduce power consumption by eliminating the need for high gain opamps. A boosted preset voltage is also introduced to improve the conversion rate without consuming more power. The ADC operates at 2.5MS/s, and near the Nyquist-rate, a prototype has a signal-to-noise and distortion ratio (SNDR) of 55.99 dB and a spurious-free dynamic-range (SFDR) of 66.85 dB. The chip was fabricated in 0. 18μm CMOS and it has an active area of 0.146mm2 and consumes 0.74mW from a 1.8V supply.
Enhancement of unsupervised feature selection for conditional random fields learning in Chinese word segmentation

This work proposed a unified view of several unsupervised feature selection based on frequent strings that improve conditional random fields (CRF) model for Chinese word segmentation (CWS). These features include character-based n-gram (CNG), accessor variety based string (AVS), term-contributed frequency (TCF), and term-contributed boundary (TCB), with a specific manner of boundary overlapping. For the experiment, the baseline is the 6-tag, a state-of-the-art labeling scheme of CRF-based CWS; and the data set is acquired from SIGHAN CWS bakeoff 2005 and SIGHAN CWS 2010. The experiment results show that all of those features improve the performance of the baseline system in terms of recall, precision, and their harmonic average as F1 measure score, on both accuracy (F) and out-of-vocabulary recognition (FOOV). In particular, this work presents a novel feature selection approach of the compound feature “AVS+TCB” that outperforms other types of features for CRF-based CSW in terms of F and FOOV.
Heterogeneity in Combined Pulmonary Fibrosis and Emphysema

Background: Combined pulmonary fibrosis and emphysema (CPFE) is a unique disorder described in several case series of upper lobe emphysema associated with lower lobe fibrosis. Patients with this entity have relatively preserved lung volumes and spirometry but marked reductions in diffusing capacity on pulmonary function testing. Smoking appears to be the predominant risk factor for this disorder. Usual interstitial pneumonia has been the most common histological pattern of interstitial lung disease described on biopsy in the literature. Objectives: To characterize the clinical, imaging and pathological features of a cohort of patients with CPFE. Methods: Retrospective review of electronic medical record data, radiological imaging, and available lung biopsy specimens for a series of 10 patients with CPFE at the Providence VA Medical Center, Providence, R.I. , USA. Results: We describe a series of 10 patients with CPFE. All had severe reductions in diffusing capacity out of proportion to their lung volumes and spirometry. All had predominantly upper lobe emphysema on computed tomography; 8/10 had lower lobe subpleural reticular abnormalities and honeycombing, while 2 had lower lobe ground glass changes on imaging. These 2 patients demonstrated a pattern of interstitial lung disease on biopsy characterized by intra-alveolar macrophage accumulation in association with marked alveolar septal fibrosis, consistent with a variant form of desquamative interstitial pneumonia with extensive fibrosis. Conclusions: The imaging findings and pathology in patients with CPFE are heterogeneous.
Robust submap-based probabilistic inconsistency detection for multi-robot mapping

The primary goal of employing multiple robots in active mapping tasks is to generate a globally consistent map efficiently. However, detecting the inconsistency of the generated global map is still an open problem. In this paper, a novel multi-level approach is introduced to measure the full 3D map inconsistency in which submap-based tests are performed at both single robot and multi-robot level. The conformance test based on submaps is done by modeling the histogram of the misalignment error metric into a truncated Gaussian distribution. Besides, the detected inconsistency is further validated through a 3D map registration process. The accuracy of the proposed method is evaluated using submaps from challenging environments in both indoor and outdoor, which illustrates its usefulness and robustness for multi-robot mapping tasks.
Cohort Query Processing

Modern Internet applications often produce a large volume of user activity records. Data analysts are interested in cohort analysis, or finding unusual user behavioral trends, in these large tables of activity records. In a traditional database system, cohort analysis queries are both painful to specify and expensive to evaluate. We propose to extend database systems to support cohort analysis. We do so by extending SQL with three new operators. We devise three different evaluation schemes for cohort query processing. Two of them adopt a non-intrusive approach. The third approach employs a columnar based evaluation scheme with optimizations specifically designed for cohort query processing. Our experimental results confirm the performance benefits of our proposed columnar database system, compared against the two non-intrusive approaches that implement cohort queries on top of regular relational databases.
Expert diagnosis of computer systems using neuro-fuzzy knowledge base

The functional diagnosis expert system based on knowledge base in the form of neuro-fuzzy network was proposed in this paper. Current values of diagnostic parameters are measured by sensors. The hybrid expert diagnostic system with neuro-fuzzy network knowledge base supports decisions in the situation when the diagnosis algorithm is not known and is formed from the initial data in the form of production rules. Sensors use to automate the process of accumulation of knowledge in the expert system. The need to take decisions in real time results the number of trees corresponding to incoming data, equal to the number of samples during the observation period. The problem of large amounts of data in determining the technical condition of the complex technical object is solved by using this data as a training sample for the knowledge base. The expert diagnosis system for assessing the PC performance was considered how the example.
Notions of Monad Strength

Over the past two decades the notion of a strong monad has found wide applicability in computing. Arising out of a need to interpret products in computational and semantic settings, different approaches to this concept have arisen. In this paper we introduce and investigate the connections between these approaches and also relate the results to monad composition. We also introduce new methods for checking and using the required laws associated with such compositions, as well as provide examples illustrating problems and issues that arise.