Miracle-dz/UniFAR-FTUs huggingface dataset:
GeneMark.hmm: new solutions for gene finding.

The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algorithms. The GeneMark. hmm algorithm presented here was designed to improve the gene prediction quality in terms of finding exact gene boundaries. The idea was to embed the GeneMark models into naturally derived hidden Markov model framework with gene boundaries modeled as transitions between hidden states. We also used the specially derived ribosome binding site pattern to refine predictions of translation initiation codons. The algorithm was evaluated on several test sets including 10 complete bacterial genomes. It was shown that the new algorithm is significantly more accurate than GeneMark in exact gene prediction. Interestingly, the high gene finding accuracy was observed even in the case when Markov models of order zero, one and two were used. We present the analysis of false positive and false negative predictions with the caution that these categories are not precisely defined if the public database annotation is used as a control.
New GFZ effective angular momentum excitation functions and their impact on nutation

Recently the Earth System Modelling Group of GeoForschungsZentrum (ESMGFZ) in Potsdam started producing a new series of Effective Angular Momentum Excitation Functions (EAM). As a novelty, the data is given in 3-hour resolution for the influence of the atmosphere and dynamic ocean, and 1-day resolution for terrestrial hydrosphere and barystatic sea-level changes. In addition to this, IERS recently started publishing their new series of C04 solution for Earth Orientation Parameters (EOP), based on new combination of all observations and ITRF2014 terrestrial frame. We use the ESMGFZ data to numerically integrate Brzeziński’s broad-band Liouville equations in celestial frame and compare the results with IERS C04 solution for celestial pole offsets in the interval 1986.0-2018.4. Alternatively, we also add a possible influence of unevenly distributed Geomagnetic jerks (GMJ). In the process of integration we look for the best-fitting parameters (period T, Q-factor) of Free Core Nutation (FCN). It is demonstrated that the fit between integrated and observed values is much better when compared with our previous solutions, based on older models of geophysical excitations. The fit is improved significantly when GMJ quasi-impulse effect is included. The best fit is obtained for atmospheric, oceanic and GMJ excitations, the preferred parameters of FCN being = 429.53 ± 0.04 , = 21600 ± 200. We also estimate new value for empirical prograde MHB Sun-synchronous correction SSC = (0.1045 + 0.0193i)e . ARTICLE INFO
A Constituent Syntactic Parse Tree Based Discourse Parser

This paper describes our system in the CoNLL-2016 shared task. Our system takes a piece of newswire text as input and returns the discourse relations. In our system we use a pipeline to conduct each subtask. Our system is evaluated on the CoNLL-2016 Shared Task closed track and obtains 0.1515 in F1 measurement, especially the part of detecting connectives, which achieves 0.9838 on blind test set.
Effect of Inactivation of the Global Oxidative Stress Regulator oxyR on the Colonization Ability of Escherichia coli O1:K1:H7 in a Mouse Model of Ascending Urinary Tract Infection

ABSTRACT To survive within the host urinary tract, Escherichia coli strains that cause urinary tract infection (UTI) presumably must overcome powerful oxidant stresses, including the oxygen-dependent killing mechanisms of neutrophils. Accordingly, we assessed the global oxygen stress regulator OxyR of Escherichia coli as a possible virulence factor in UTI by determining the impact of oxyR inactivation on experimental urovirulence in CBA/J and C57BL (both wild-type and p47phox−/−) mice. The oxyR and oxyS genes of wild-type E. coli strain Ec1a (O1:K1:H7) were replaced with a kanamycin resistance cassette to produce an oxyRS mutant. During in vitro growth in broth or human urine, the oxyRS mutant exhibited the same log-phase growth rate (broth) and plateau density (broth and urine) as Ec1a, despite its prolonged lag phase (broth) or initial decrease in concentration (urine). The mutant, and oxyRS mutants of other wild-type ExPEC strains, exhibited significantly increased in vitro susceptibility to inhibition by H2O2, which, like the altered growth kinetics observed with oxyRS inactivation, were reversed by restoration of oxyR on a multiple-copy-number plasmid. In CBA/J mice, Ec1a significantly outcompeted its oxyRS mutant (by >1 log10) in urine, bladder, and kidney cultures harvested 48 h after perurethral inoculation of mice, whereas an oxyR-complemented mutant exhibited equal or greater colonizing ability than that of the parent. Although C57BL mice were less susceptible to experimental UTI than CBA/J mice, wild-type and p47phox−/− C57BL mice were similarly susceptible, and the oxyR mutant of Ec1a was similarly attenuated in C57BL mice, regardless of the p47phox genotype, as in CBA/J mice. Within the E. coli Reference collection, 94% of strains were positive for oxyR. These findings fulfill the second and third of Koch's molecular postulates for oxyR as a candidate virulence-facilitating factor in E. coli and indicate that oxyR is a broadly prevalent potential target for future preventive interventions against UTI due to E. coli. They also suggest that neutrophil phagocyte oxidase is not critical for defense against E. coli UTI and that the major oxidative stresses against which OxyR protects E. coli within the host milieu are not phagocyte derived.
Advanced Character Recognition 6610 Grading: Five Programming Assignments Term Paper Final Examination Syllabus 1. Review: Intro to Ocr (ecse 2610)

ECSE 6610 Advanced Character Recognition. Principles and practice of the recognition of isolated or connected typeset, hand-printed, and cursive characters. Review of optical digitization, supervised and unsupervised estimation of classifier parameters, bias and variance, expectation maximization, the curse of dimensionality. Advanced classification techniques including classifier combinations, support vector machines, hidden Markov methods, styles, language context, adaptation, segmentation-free classifiers, indirect symbolic correlation. Prereq: ECSE 2610, Probability, Linear Algebra. Spring term annually.
A Content Analysis Technique for Inconsistency Detection in Software Requirements Documents

This paper presents J-RAn (Java Requirement Analyzer), a tool that implements a novel Content Analysis technique to support the verification of consistency and completeness of a Software Requirement Specification. This technique exploits the extraction, from a requirement document, of the interactions between the entities described in the document as Subject-Action-Object (SAO) triples (obtainable using a suitable syntactic parser). SAO triples represent a concept in its most synthesizing form. Analyzing the distribution of such concepts in the requirement document helps to locate possible sources of inconsistency and incompleteness.
Archaea and the prokaryote-to-eukaryote transition.

Since the late 1970s, determining the phylogenetic relationships among the contemporary domains of life, the Archaea (archaebacteria), Bacteria (eubacteria), and Eucarya (eukaryotes), has been central to the study of early cellular evolution. The two salient issues surrounding the universal tree of life are whether all three domains are monophyletic (i.e., all equivalent in taxanomic rank) and where the root of the universal tree lies. Evaluation of the status of the Archaea has become key to answering these questions. This review considers our cumulative knowledge about the Archaea in relationship to the Bacteria and Eucarya. Particular attention is paid to the recent use of molecular phylogenetic approaches to reconstructing the tree of life. In this regard, the phylogenetic analyses of more than 60 proteins are reviewed and presented in the context of their participation in major biochemical pathways. Although many gene trees are incongruent, the majority do suggest a sisterhood between Archaea and Eucarya. Altering this general pattern of gene evolution are two kinds of potential interdomain gene transferrals. One horizontal gene exchange might have involved the gram-positive Bacteria and the Archaea, while the other might have occurred between proteobacteria and eukaryotes and might have been mediated by endosymbiosis.
Amorphous and Polycrystalline Photoconductors for Direct Conversion Flat Panel X-Ray Image Sensors

In the last ten to fifteen years there has been much research in using amorphous and polycrystalline semiconductors as x-ray photoconductors in various x-ray image sensor applications, most notably in flat panel x-ray imagers (FPXIs). We first outline the essential requirements for an ideal large area photoconductor for use in a FPXI, and discuss how some of the current amorphous and polycrystalline semiconductors fulfill these requirements. At present, only stabilized amorphous selenium (doped and alloyed a-Se) has been commercialized, and FPXIs based on a-Se are particularly suitable for mammography, operating at the ideal limit of high detective quantum efficiency (DQE). Further, these FPXIs can also be used in real-time, and have already been used in such applications as tomosynthesis. We discuss some of the important attributes of amorphous and polycrystalline x-ray photoconductors such as their large area deposition ability, charge collection efficiency, x-ray sensitivity, DQE, modulation transfer function (MTF) and the importance of the dark current. We show the importance of charge trapping in limiting not only the sensitivity but also the resolution of these detectors. Limitations on the maximum acceptable dark current and the corresponding charge collection efficiency jointly impose a practical constraint that many photoconductors fail to satisfy. We discuss the case of a-Se in which the dark current was brought down by three orders of magnitude by the use of special blocking layers to satisfy the dark current constraint. There are also a number of polycrystalline photoconductors, HgI2 and PbO being good examples, that show potential for commercialization in the same way that multilayer stabilized a-Se x-ray photoconductors were developed for commercial applications. We highlight the unique nature of avalanche multiplication in a-Se and how it has led to the development of the commercial HARP video-tube. An all solid state version of the HARP has been recently demonstrated with excellent avalanche gains; the latter is expected to lead to a number of novel imaging device applications that would be quantum noise limited. While passive pixel sensors use one TFT (thin film transistor) as a switch at the pixel, active pixel sensors (APSs) have two or more transistors and provide gain at the pixel level. The advantages of APS based x-ray imagers are also discussed with examples.
Generating Class-Based Test Cases for Interface Classes of Object-Oriented Black Box Frameworks

An application framework provides a reusable design and implementation for a family of software systems. Application developers extend the framework to build their particular applications using hooks. Hooks are the places identified to show how to use and customize the framework. Hooks define the Framework Interface Classes (FICs) and their possible specifications, which helps in building reusable test cases for the implementations of these classes. This paper introduces a novel technique called all paths-state to generate state-based test cases to test the FICs at class level. The technique is experimentally evaluated. The empirical evaluation shows that all paths-state technique produces test cases with a high degree of coverage for the specifications of the implemented FICs comparing to test cases generated using round-trip path and all-transition techniques. Keywords—Hooks, object-oriented framework, framework interface classes (FICs), specification-based testing, test case generation.
Tractable Bayesian Learning of Tree Augmented Naive Bayes Models

Bayesian classifiers such as Naive Bayes or Tree Augmented Naive Bayes (TAN) have shown excellent performance given their simplicity and heavy underlying independence assumptions. In this paper we introduce a classifier taking as basis the TAN model and taking into account uncertainty in model selection. To do this we introduce decomposable distributions over TANs and show that they allow the expression resulting from the Bayesian model averaging of TAN models to be integrated into closed form. With this result we construct a classifier with a shorter learning time and a longer classification time than TAN. Empirical results show that the classifier is, most of the cases, more accurate than TAN and approximates better the class probabilities.
Evaluation of a Bundling Technique for Parallel Coordinates

We describe a technique for bundled curve representations in parallel-coordinates plots and present a controlled user study evaluating their effectiveness. Replacing the traditional C^0 polygonal lines by C^1 continuous piecewise Bezier curves makes it easier to visually trace data points through each coordinate axis. The resulting Bezier curves can then be bundled to visualize data with given cluster structures. Curve bundles are efficient to compute, provide visual separation between data clusters, reduce visual clutter, and present a clearer overview of the dataset. A controlled user study with 14 participants confirmed the effectiveness of curve bundling for parallel-coordinates visualization: 1) compared to polygonal lines, it is equally capable of revealing correlations between neighboring data attributes; 2) its geometric cues can be effective in displaying cluster information. For some datasets curve bundling allows the color perceptual channel to be applied to other data attributes, while for complex cluster patterns, bundling and color can represent clustering far more clearly than either alone.
Effects of ADAM10 upregulation on progression, migration, and prognosis of nasopharyngeal carcinoma

A disintegrin and metalloprotease 10 (ADAM10) is a typical member of the ADAMs family, which has been reported to be upregulated in various types of cancers and contribute to cancer progression and metastasis. However, little is known about the role of ADAM10 in nasopharyngeal carcinoma (NPC). The purpose of this study is to explore ADAM10 expression status and its biological functions in NPC. We first examined the expression of ADAM10 in NPC tissues and cell lines by immunohistochemistry, Western blotting, PCR, and immunofluorescence analysis. We observed that ADAM10 was significantly elevated in NPC and its expression level was correlated with T classification (P = 0.044), distant metastasis (P = 0.016), TNM clinical stage (P = 0.013), and proliferation marker Ki‐67 expression (P = 0.001). Patients with NPC with high expression of ADAM10 had shorter overall survival rates. In addition, knockdown of ADAM10 by RNAi was found to inhibit the CNE‐2 cell proliferation and migration. Our findings hinted that overexpression of ADAM10 promotes the progression and migration of NPC, which makes it a potential therapeutic target for the treatment of tumor metastases in NPC.
Quantitative Measurement of C6 Antibody following Antibiotic Treatment of Borrelia burgdorferi Antibody-Positive Nonclinical Dogs

ABSTRACT The detection of antibody to the Borrelia burgdorferi C6 peptide by use of enzyme-linked immunoassays is a widely accepted method for the diagnosis of Lyme disease spirochete infection in dogs and in humans. Antibody to the C6 peptide is highly specific for B. burgdorferi and declines following treatment of dogs and humans exposed to B. burgdorferi. A quantitative assay for determining C6 antibody levels was developed and used to measure changes in antibody levels following antibiotic treatment of B. burgdorferi antibody-positive nonclinical dogs. One hundred thirty-two client-owned dogs were used in the study; 64 were negative, 53 of 68 positive animals received treatment, and 15 were untreated controls. Test sera were collected at 3, 6, and 12 months from seropositive dogs receiving treatment and untreated controls. Dogs in the treated group were assigned to moderate-to-high (≥29 U/ml)- and low (<29 U/ml)-C6-level groups because the change in the C6 level after treatment was dependent on the level prior to treatment. There were significant declines in the 30 dogs with moderate-to-high initial C6 levels that exceeded the maximal declines of the untreated control dogs in all cases at 6 months (16 data points) and 12 months (29 data points) posttreatment. There was little change in C6 level following antibiotic therapy in the 23 dogs with low initial C6 levels. The quantitative C6 antibody test can be used to measure changes in C6 antibody levels following treatment of antibody-positive nonclinical dogs.
Millennial-scale denudation rates in the Himalaya of Far Western Nepal

Abstract. The Himalayas stretch ∼3000 km along the Indo-Eurasian plate boundary. Along-strike variations in the fault geometry of the Main Himalayan Thrust (MHT) have given rise to significant variations in the topographic steepness, exhumation rate, and orographic precipitation along the Himalayan front. Over the past 2 decades, the rates and patterns of Himalayan denudation have been documented through numerous cosmogenic nuclide measurements in central and eastern Nepal, Bhutan, and northern India. To date, however, few denudation rates have been measured in Far Western Nepal, a ∼300 km wide region near the center of the Himalayan arc, which presents a significant gap in our understanding of Himalayan denudation. Here we report new catchment-averaged millennial-scale denudation rates inferred from cosmogenic 10Be in fluvial quartz at seven sites in Far Western Nepal. The inferred denudation rates range from 385±31 t km−2 yr−1 (0.15±0.01 mm yr−1) to 8737±2908 t km−2 yr−1 (3.3±1.1 mm yr−1) and, in combination with our analyses of channel topography, are broadly consistent with previously published relationships between catchment-averaged denudation rates and normalized channel steepness across the Himalaya. These data show that the denudation rate patterns in Far Western Nepal are consistent with those observed in central and eastern Nepal. The denudation rate estimates from Far Western Nepal show a weak correlation with catchment-averaged specific stream power, consistent with a Himalaya-wide compilation of previously published stream power values. Together, these observations are consistent with a dependence of denudation rate on both tectonic and climatic forcings, and they represent a first step toward filling an important gap in denudation rate measurements in Far Western Nepal.
Revision bioestratigrafica del Albiano inferior a superior basal en la Cuenca Andina peruana (Peru central y norte).

The study of the ammonite fauna of the Lower to Early Upper Albian formations allow a major revision of the biostratigraphic frame of Northern and Central Peru. A new subdivision in ammonites zones, subzones and bio-horizons terms is proposed. The Lower Albian is represented by the Nicholsoni Biozone (subdivided into the umbilicostatus and nicholsoni biohorizons, followed by an Interval Subzone) and by the Raimondii Biozone (carved in three subzones: Haasi, Raimondii - itself divided into the ebrayi and alternum biohorizons and Mathewsi, including the pseudolyelli biohorizon). The Middle Albian is characterized by the Carbonarium Biozone, carved in the Ulrichi and Carbonarium Subzones. The base of the Upper Albian is represented by the Cristatum Subzone.
The Great Moderation and the Risk of Inflation: A View From Developing Countries

It is an honor to be a keynote speaker at this important gathering. Personally, this is a special meeting as I contributed, together with Barry Eichengreen, Takatoshi Ito, and Charles Wyplosz, to the writing of the first report for this series of conferences back in 1999. It was lots of fun and an intellectual pleasure to work with such a great team of colleagues, and in such an important issue. In that first Geneva Report we wrote about the need to reform the IMF giving it independence, such as what we praise for central banks, and accountability, an essential element to make independence effective. In the future I would like to develop further on those issues; however, today I will focus on an even more pressing debate in the recent macro juncture: monetary policy, stability and the current risks of an outburst of inflation around the world, which is precisely the subject of this conference.
Instantaneous Frequency Estimation Using Fractional Fourier Transform and Wigner Distribution

This paper presents a novel Instantaneous Frequency (IF) estimation technique based on Signal separation and Wigner distribution (WD). WD is widely used for IF estimation of mono-component signals Proposed technique extends WD based IF estimation technique to multi-component signals. The Proposed technique decomposes a signal into its components using a hybrid image processing and fractional filtering based technique. WD with adaptive data driven window length is then used for instantaneous frequency estimation of mono-component separated signal components. Experiment results demonstrate that proposed scheme performs reasonably well for moderate to high Signal to Noise ratios (SNR).
Using cellzilla for plant growth simulations at the cellular level

Cellzilla is a two-dimensional tissue simulation platform for plant modeling utilizing Cellerator arrows. Cellerator describes biochemical interactions with a simplified arrow-based notation; all interactions are input as reactions and are automatically translated to the appropriate differential equations using a computer algebra system. Cells are represented by a polygonal mesh of well-mixed compartments. Cell constituents can interact intercellularly via Cellerator reactions utilizing diffusion, transport, and action at a distance, as well as amongst themselves within a cell. The mesh data structure consists of vertices, edges (vertex pairs), and cells (and optional intercellular wall compartments) as ordered collections of edges. Simulations may be either static, in which cell constituents change with time but cell size and shape remain fixed; or dynamic, where cells can also grow. Growth is controlled by Hookean springs associated with each mesh edge and an outward pointing pressure force. Spring rest length grows at a rate proportional to the extension beyond equilibrium. Cell division occurs when a specified constituent (or cell mass) passes a (random, normally distributed) threshold. The orientation of new cell walls is determined either by Errera's rule, or by a potential model that weighs contributions due to equalizing daughter areas, minimizing wall length, alignment perpendicular to cell extension, and alignment perpendicular to actual growth direction.