Miracle-dz/UniFAR-FTUs huggingface dataset:
Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2

Abstract AID deaminates C to U in either strand of Ig genes, exclusively producing C:G/G:C to T:A/A:T transition mutations if U is left unrepaired. Error-prone processing by UNG2 or mismatch repair diversifies mutation, predominantly at C:G or A:T base pairs, respectively. Here, we show that transversions at C:G base pairs occur by two distinct processing pathways that are dictated by sequence context. Within and near AGCT mutation hotspots, transversion mutation at C:G was driven by UNG2 without requirement for mismatch repair. Deaminations in AGCT were refractive both to processing by UNG2 and to high-fidelity base excision repair (BER) downstream of UNG2, regardless of mismatch repair activity. We propose that AGCT sequences resist faithful BER because they bind BER-inhibitory protein(s) and/or because hemi-deaminated AGCT motifs innately form a BER-resistant DNA structure. Distal to AGCT sequences, transversions at G were largely co-dependent on UNG2 and mismatch repair. We propose that AGCT-distal transversions are produced when apyrimidinic sites are exposed in mismatch excision patches, because completion of mismatch repair would require bypass of these sites.
Effects of Legal Status and Health Service Availability on Mortality

Using a straight-forward Differences-in-Differences approach, effects of the 1986 Immigration Reform and Control Act and the 1986 and 1987 Omnibus Budget Reconciliation Acts on mortality levels in California are examined. These acts had the effect of legalizing and granting healthcare coverage to millions of previously illegal immigrants. Utilizing data on all IRCA applicants and all California deaths within this time period, I find evidence of substantial declines in mortality correlated with the size of the legalized cohort by county. If we assume, for purposes of a back of the envelope calculation, that after the reform IRCA applicants’ mortality rate is approximately equal to that of demographically similar California residents, this finding is consistent with IRCA applicants being subject to five to six times the mortality rate of California residents prior to the reform.
HARMONIC POWER FLUX METHOD EMPHASIS ON COMPLEX SOUNDS FOR MIREX 2012 ONSET DETECTION

This extended abstract proposes a new method for onset detection using harmonic information on each note. Especially, this method is optimized on sudden attack instrument family. Even though there are some exceptions such as missing fundamentals in piano first octave notes or only existence of even harmonics in clarinet, each note in music has integer multiple harmonics in common. This method outperforms about 5 and 17% in F-measure than existing algorithms such as spectral flux or spectral difference.
Verifiable and private top-k monitoring

In a data streaming model, records or documents are pushed from a data owner, via untrusted third-party servers, to a large number of users with matching interests. The match in interest is calculated from the correlation between each pair of document and user query. For scalability and availability reasons, this calculation is delegated to the servers, which gives rise to the need to protect the privacy of the documents and user queries. In addition, the users need to guard against the eventuality of a server distorting the correlation score of the documents to manipulate which documents are highlighted to certain users. In this paper, we address the aforementioned privacy and verifiability challenges. We introduce the first cryptographic scheme which concurrently safeguards the privacy of the documents and user queries in such a data streaming model, while enabling users to verify the correlation scores obtained. We provide techniques to bound the computation demand in decrypting the correlation scores, and we demonstrate the overall practicality of the scheme through experiments with real data.
Corpus Based Method of Transforming Nominalized Phrases into Clauses for Text Mining Application

Nominalization is a linguistic phenomenon in which events usually described in terms of clauses are expressed in the form of noun phrases. Extracting event structures is an important task in text mining applications. To achieve this goal, clauses are parsed and the argument structure of main verbs are extracted from the parsed results. This kind of preprocessing has been commonly done in the past research. In order to extract event structure from nominalized phrases as well, we need to establish a technique to transform nominalized phrases into clauses. In this paper, we propose a method to transform nominalized phrases into clauses by using corpus-based approach. The proposed method first enumerates possible predicate/argument structures by referring to a nominalized phrase (noun phrase) and makes their ranking based on the frequency of each argument in the corpus. The algorithm based on this method was evaluated using a corpus consisting of 24,626 aviation safety reports in English and it achieved a 78% accuracy in transformation. The algorithm was also evaluated by applying a text mining application to extract events and their cause-effect relations from the texts. This application produced an improvement in the text mining application’s performance. key words: nominalization, predicate/argument structure, text mining, corpus based method
Reproductive Health and the Millennium Development Goals: Politics, Ethics, Evidence and an ‘Unholy Alliance’

This paper provides a chronological account of the evolution of the concept and policy of reproductive health and its initial entry, and subsequent exclusion, from UN declarations. In the 1990s effective lobbying by sexual and reproductive rights activists established reproductive health for all as a UN goal. However, at the Millennium Assembly of 2000 and in the Millennium Development Goals (MDGs), an ‘unholy alliance’ of the Holy See and a handful of conservative Muslim governments managed to keep reproductive health off the agenda. This was successful political manoeuvring for the short-term, but the alliance fell apart and the power of the theoretical and empirical case in support of reproductive health saw it return to the MDGs in 2005. The moral standing of religious institutions, such as the Holy See, is undermined by such opportunistic, short-term political behaviour and, in particular, the ambiguous legal status of the Holy See at the UN is called into question.
Fabrication and Testing of Viscosity Measuring Instrument ( Viscometer )

This paper presents the fabrication and testing of a simple and portable viscometer for the measurement of bulk viscosity of different Newtonian fluids. It is aimed at making available the instrument in local markets and consequently reducing or eliminating the prohibitive cost of importation. The method employed is the use of a D.C motor to rotate a disc having holes for infra-red light to pass through and fall on a photo-diode thus undergoing amplification and this signal being translated on a moving-coil meter as a deflection. The motor speed is kept constant but varies with changes in viscosity of the fluid during stirring, which alter signals being read on the meter. The faster is revolution per minute of the disc, the less the deflection on the meter and vise-versa. From the results of tests conducted on various sample fluids using data on standard Newtonian fluids as reliable guide the efficiency of the viscometer was 76.5%.
Efficient similarity search using the Earth Mover's Distance for large multimedia databases

Multimedia similarity search in large databases requires efficient query processing. The Earth mover's distance, introduced in computer vision, is successfully used as a similarity model in a number of small-scale applications. Its computational complexity hindered its adoption in large multimedia databases. We enable directly indexing the Earth mover's distance in structures such as the R-tree and the VA-file by providing the accurate 'MinDist' function to any bounding rectangle in the index. We exploit the computational structure of the new MinDist to derive a new lower bound for the EMD MinDist which is assembled from quantized partial solutions yielding very fast query processing times. We prove completeness of our approach in a multistep scheme. Extensive experiments on real world data demonstrate the high efficiency.
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data

UNLABELLED Estimating pairwise correlation from replicated genome-scale (a.k.a. OMICS) data is fundamental to cluster functionally relevant biomolecules to a cellular pathway. The popular Pearson correlation coefficient estimates bivariate correlation by averaging over replicates. It is not completely satisfactory since it introduces strong bias while reducing variance. We propose a new multivariate correlation estimator that models all replicates as independent and identically distributed (i.i.d.) samples from the multivariate normal distribution. We derive the estimator by maximizing the likelihood function. For small sample data, we provide a resampling-based statistical inference procedure, and for moderate to large sample data, we provide an asymptotic statistical inference procedure based on the Likelihood Ratio Test (LRT). We demonstrate advantages of the new multivariate correlation estimator over Pearson bivariate correlation estimator using simulations and real-world data analysis examples. AVAILABILITY The estimator and statistical inference procedures have been implemented in an R package 'CORREP' that is available from CRAN [http://cran.r-project.org] and Bioconductor [http://www.bioconductor. org/]. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Algorithm and architecture for high speed merged arithmetic FIR filter generation

This paper presents a new method and an algorithm for the synthesis of a high-speed variable coefficients Finite Impulse Response (FIR) filter. Timing performance and reduced area are achieved employing two techniques. Firstly, a merged arithmetic architecture is used to synthesize the FIR filter function directly. Secondly, an algorithm that looks for minimum delay Partial Product Reduction Tree (PPRT) is developed. These results are combined to create a program that furnishes a speed optimized netlist for the filter. The performance of the proposed method has been evaluated by comparing it to the result achieved by cell-based synthesis software.
Akonni TruTip® and Qiagen® Methods for Extraction of Fetal Circulating DNA - Evaluation by Real-Time and Digital PCR

Due to the low percentage of fetal DNA present in maternal plasma (< 10%) during early gestation, efficient extraction processes are required for successful downstream detection applications in non-invasive prenatal diagnostic testing. In this study, two extraction methods using similar chemistries but different workflows were compared for isolation efficiency and percent fetal DNA recovery. The Akonni Biosystems TruTip technology uses a binding matrix embedded in a pipette tip; the Circulating Nucleic Acids Kit from Qiagen employs a spin column approach. The TruTip method adds an extra step to decrease the recovery of DNA fragments larger than 600 bp from the sample to yield an overall higher percentage of smaller molecular weight DNA, effectively enriching for fetal DNA. In this evaluation, three separate extraction comparison studies were performed - a dilution series of fragmented DNA in plasma, a set of clinical maternal samples, and a blood collection tube time point study of maternal samples. Both extraction methods were found to efficiently extract small fragment DNA from large volumes of plasma. In the amended samples, the TruTip extraction method was ~15% less efficient with overall DNA recovery, but yielded an 87% increase in % fetal DNA relative to the Qiagen method. The average percent increase of fetal DNA of TruTip extracted samples compared to the Qiagen method was 55% for all sets of blinded clinical samples. A study comparing extraction efficiencies from whole blood samples incubated up to 48 hours prior to processing into plasma resulted in more consistent % fetal DNA recoveries using TruTip. The extracted products were tested on two detection platforms, quantitative real-time PCR and droplet digital PCR, and yielded similar results for both extraction methods.
A Risk-Adjusted Evaluation Of The JSE Top 40 As An International Investment Option

In response to the wealth destruction caused by the 2007/2008 global financial crisis, many developed economies have lowered their interest rates to improve their balance sheets (SARB, 2008-2012). However, in order for investors to sustain expected returns they will have to deviate from the traditional approach of investing in government bonds and consider investing in emerging markets, which are considered as potential drivers of global growth (Deloitte Consulting LLP, 2012). The goal of this paper is to establish the importance of considering South Africa as an emerging market investment opportunity, but also to acknowledge its ability of outperforming several other common emerging markets during the post-financial crisis period. This was done by means of a novel approach to the Omega ratio. The results from this paper confirms this, illustrating that the performance of the JSE Top 40 will compensate for the additional political risk that emerging market investments possess (Anshuman, 2010).
Late language emergence in 24-month-old twins: heritable and increased risk for late language emergence in twins.

PURPOSE This study investigated the etiology of late language emergence (LLE) in 24-month-old twins, considering possible twinning, zygosity, gender, and heritability effects for vocabulary and grammar phenotypes. METHOD A population-based sample of 473 twin pairs participated. Multilevel modeling estimated means and variances of vocabulary and grammar phenotypes, controlling for familiality. Heritability was estimated with DeFries-Fulker regression and variance components models to determine effects of heritability, shared environment, and nonshared environment. RESULTS Twins had lower average language scores than norms for single-born children, with lower average performance for monozygotic than dizygotic twins and for boys than girls, although gender and zygosity did not interact. Gender did not predict LLE. Significant heritability was detected for vocabulary (0.26) and grammar phenotypes (0.52 and 0.43 for boys and girls, respectively) in the full sample and in the sample selected for LLE (0.42 and 0.44). LLE and the appearance of Word Combinations were also significantly heritable (0.22-0.23). CONCLUSIONS The findings revealed an increased likelihood of LLE in twin toddlers compared with single-born children that is modulated by zygosity and gender differences. Heritability estimates are consistent with previous research for vocabulary and add further suggestion of heritable differences in early grammar acquisition.
VISUAL AIDS FOR CATALOGING AND CODE GENERATION FOR SGML-BASED DOCUMENTS OF DESIGN PATTERNS

Design patterns are abstract software components for system structures and functions used in OOA/OOD. A pattern has a structure in its semantics, however it is described currently in an informal way with plain texts, gures, and pseudo codes. Towards cataloging design patterns on computers, we have designed a structured document framework for patterns which re ects the semantic structure. This framework is based on SGML (Standard General Markup Language), and describes plain texts, con guration information for chart generation and code generation, and pseudo codes in a uni ed and integrated form. Our prototype of the design pattern catalog system is for Java software, and written in Java. It has three components: SGMLDB, Browser, and Class Code Generator. This paper focuses on the browser, and the code generator. The browser converts a requested part of an SGML-based pattern document into HTML for browsing, generating anchors automatically to link to other HTML pages of patterns and corresponding class codes. It also generates gures of OMT charts automatically from the con guration information.
Women Incidence of Type 2 Diabetes in Young and Middle-Aged Sugar-Sweetened Beverages , Weight Gain , and Correction

Correction Contact me if this article is corrected. Citations Contact me when this article is cited. This article has been cited 254 times. Topic collections Contact me when new articles are published in these topic areas. Diseases; Diabetes Mellitus Public Health; Obesity; Women's Health; Women's Health, Other; Endocrine Related Letters . ;293():422. JAMA et al. In Reply: . ;293():422. JAMA et al. Sugar-Sweetened Beverages, Weight Gain, and Diabetes
Using Heuristic Rules to Improve Persian Part of Speech Tagging Accuracy

One of the major activities in Natural Language Processing is determining a word’s part of speech (POS) tag. In this research we focus on improving the accuracy of Persian part of speech tagging by applying post processing heuristic rules. To evaluate the effects of those rules we use Bijankhan tagged corpus and for tagging, Maximum Likelihood Estimation (MLE) approach is selected because of its simplicity and the ease of implementation. Furthermore, we have studied the effect of size of training on the accuracy of the MLE method. The experimental results show that the heuristic rules improve the accuracy especially for the unknown words 1 .
Nonstandard Models in Recursion Theory and Reverse Mathematics

We give a survey of the study of nonstandard models in recursion theory and reverse mathematics. We discuss the key notions and techniques in effective computability in nonstandard models, and their applications to problems concerning combinatorial principles in subsystems of second order arithmetic. Particular attention is given to principles related to Ramsey’s Theorem for Pairs.
Eco-Environmental Sound Classification Based on Matching Pursuit and Support Vector Machine

Research on various eco-environmental sounds is very important for people to understand a particular area. However, eco-environmental sounds have many specific properties such as the diversity, high background noise and non-stationary structure which make many traditional audio features hard to characterize them accurately. In this paper, a novel feature extraction technique based on Matching Pursuit algorithm is adopted to obtain proper features which can describe the specific properties of eco-environment sounds accurately. In order to further improve the performance of our classification system, we make use of the support vector machine to automatically classify the eco-environmental sounds into seven classes. The experimental results show that our system is effective to classify the environmental sounds quickly and accurately.
High sensitive DCPD measurement and analysis system of high-voltage storage capacitor

Partial discharge detection under DC is an appropriate method for insulation condition estimation. This paper presented a DCPD measurement and analysis system. System, characterized by high signal to noise ratio and strong ability for interference suppression, was composed with narrowband RLC balanced detection circuit, gain-stable amplifier and band-pass filter. Through trigger acquisition, DCPD signal was transferred to the computer and data were processed based on Δt analysis method in order to reflect characteristic parameters of PD signal by spectrum and fingerprint. Through the calibration by standard pulse generator, sensitivity of whole system reached 2pC which is enough to detect PD current in storage capacitor. Based on this measurement and analysis system, measurement for high-voltage storage capacitor with typical defects would be conducted and the results effectively reflected relationship of PD parameters. Therefore, the establishment of this system settled a good basis for defect types recognition and aging degree estimation of capacitors.
Vision-based lane departure detection system in urban traffic scenes

A lane-departure detection system without intrinsic and extrinsic camera parameters calibration is proposed in this paper. The proposed system, which provides driving safety by lane detection and lane departure warning, is focused on urban road with complicated lane marks instead of simple highway scenes. Due to the complexity of urban traffic scenes, false lane detections are highly caused by warning lines and signs whose shape and color are similar to the lane boundary. In this study, two lane features, lane width and lane boundary continuity, are proposed to obtain reliable and quality lane detected results on urban traffic scenes. Lane departure warning decisions are then applied to provide driving safety. Experimental results of urban road sceneries have demonstrated feasibility and robustness of the proposed method.
Antipatterns: A Compendium of Bad Practices in Software Development Processes

This Article presents a set of software process antipatterns, which arise as a result of bad practices within application development processes. Process AntiPatterns warn us about the harmful effects that may arise in projects, and also describe the features that identify them. The proposed anti- patterns provide a catalog that serves as a vocabulary for communication among project participants. Such Antipatterns can be implemented through software tools in order to keep better record of their implementation. Additionally, a tool that can operate under GPL (General Public license) is provided for this purpose. he goal of software development is to generate products with high levels of productivity and efficiency that ensure good levels of quality. To achieve this, it is necessary to avoid the risks introduced by bad practices of software. These bad practices have been labeled as anti-patterns, and occur in different areas. The catalog of antipatterns is an important road map, particularly on dark paths that might be followed when precautions are not taken, and of course, that cause problems in projects. This article presents a list of harmful practices that represent anti-patterns in the implementation of software development processes.
Characteristics of At-Risk Students: Opinions of Elementary and Secondary School Teachers

This study focused on a major problem facing today’s educators: high school dropouts. Research questions addressed differences in teacher perspectives of the characteristics of struggling students. Differences in teachers’ perspectives based on teaching level (elementary & secondary) were examined. The researcher conducted focus groups with a total of 12 teachers. The research was conducted in two suburban districts. Focus group questions were designed following a survey administered to 108 suburban public school teachers. The survey responses reported previously identified four dimensions of characteristics of at-risk students: behavior, achievement, family involvement, and family background. The data from the focus groups can be used to inform decisions regarding the identification and support of at-risk students. Purpose of the Study The purpose of this study was to examine perspectives of public school teachers at elementary, middle, and high school levels in hopes of providing information to assist with identifying students at-risk for dropping out of school at the earliest age possible. This study investigated teacher perspectives regarding at-risk students by addressing the following questions: (1) What are the perspectives of elementary and secondary (middle and high school) teachers with respect to characteristics of at-risk students? (2) Is there a significant difference between perspectives of public school teachers (elementary and secondary) with respect to characteristics of at-risk students? Theoretical Framework The rate at which students drop out of school has remained about the same for the past 30 years. However, in today’s workforce, dropouts are far less likely to obtain a stable job than in past generations (Monrad, 2007). More than half a million young people drop