Miracle-dz/UniFAR-FTUs huggingface dataset:
Paraoxonase1 Genetic Polymorphisms in a Mixed Ancestry African Population

Paraoxonase 1 (PON1) activity is markedly influenced by coding polymorphisms, Q/R at position 192 and M/L at position 55 of the PON1 gene. We investigated the frequencies of these polymorphisms and their effects on PON1 and antioxidant activities in 844 South African mixed ancestry individuals. Genotyping was done using allele-specific TaqMan technology, PON1 activities were measured using paraoxon and phenylacetate, oxidative status was determined by measuring the antioxidant activities of ferric reducing antioxidant power and trolox equivalent antioxidant capacity, and lipid peroxidation markers included malondialdehyde and oxidized LDL. The frequencies of Q192R and L55M were 47.6% and 28.8%, respectively, and the most common corresponding alleles were 192R (60.4%) and 55M (82.6%). The Q192 was significantly associated with 5.8 units' increase in PON1 concentration and 15.4 units' decrease in PONase activity after adjustment for age, sex, BMI, and diabetes, with suggestion of differential effects by diabetes status. The PON1 L55 variant was associated with none of the measured indices. In conclusion, we have shown that the Q192R polymorphism is a determinant of both PON1 concentration and activity and this association appeared to be enhanced in subjects with diabetes.
Using Genetic Algorithms to Repair JUnit Test Cases

JUnit test repair has been proposed as a way to alleviate the burden of maintaining the broken tests caused by evolving software. Existing techniques for JUnit test repair either focus on repairing failing assertions or fixing test case compilation errors rendered by evolving method declarations. The empirical work suggests that the synthesis of new method calls is often needed when repairing test cases in practice. In this work, we propose Test Fix, an approach to fix broken JUnit test cases by synthesizing new method calls. Test Fix reduces the synthesis to a search problem and uses a genetic algorithm to solve it. Evaluated on real world applications, preliminary experimental results show that Test Fix can repair broken tests with adding or deleting method calls. Evaluations on the performance of JUnit test repair technique using a genetic algorithm against a random search algorithm are also conducted. Experimental results indicate the clear superiority of genetic algorithms over random search algorithm.
Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina

The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.
Full-text search in email archives using social evaluation, attached and linked resources

Emails are important tools for communication and cooperation, they contain large amount of information and connections to knowledge and data sources. Because of this, it is very important to improve the efficiency of their processing. This paper describes an email search system which integrates full-text search with social search while processing also the attached and linked resources. The project described in this paper is still in progress. Due to this fact, some proposed parts of the system are not implemented and also not proven yet. The proposed equation for determining the social importance of an email has also to be tuned during the last phases of the development and the evaluation phase. The already implemented part of the system includes content extraction from the email messages, attached and linked resources and also the textual search and social relation extraction is implemented. The next phase of the development includes tuning of the social evaluation and it's integration with textual search.
Scalability of DNA sequence database on low-end cluster using Hadoop

Publicly available DNA sequence database such as GenBank managed by National Center for Biotechnology Information (NCBI) is very large and still grows exponentially. The sequence data are stored in flat file format grouped in various division based on the source taxonomy. Bacterial division alone consists of more than 100 files has size about 6 Gigabytes in total. Searching in 100 files using single server took time about 1500 seconds in a Quad Cores machine. An effort to speed up this process has been worked out by uploading the bacterial sequence data on Hadoop Distributed File System on low-end cluster. MapReduce computation model is invoked for searching algorithm in conjunction with Hadoop Distributed File System as both technologies are main component of Hadoop framework. Scalability evaluation has been performed to investigate whether increasing number of node in the cluster will be fruitful.
“ Monetary Rules for Peru ”

Properties of explicit monetary rules for Peru that specify monthly adjustments in the monetary base are examined, by conducting counterfactual historical simulations with VAR models over 1994-1999. Two alternative rules are considered for the analysis: one with nominal GDP growth as target variable and the other with inflation. The simulation results indicate that the rule with inflation as target fits better its target path, especially when it is defined as core inflation, and shows lower variability of the instrument variable. A forward-looking scheme is also tested in an implicit version of the rule with inflation as target, following the Svensson’s approach (1998). We find that explicit rules provide better fit to the target than the implicit ones. Finally, counterfactual historical analysis of the type utilized by Stuart (1996) is conducted to evaluate monetary policy in Peru. For this purpose, actual settings of monetary base during the period of analysis are contrasted with the values that would have been specified by the rule with inflation target in response to prevailing conditions. According to this comparison, monetary policy in Peru was too loose over the period January 1994 June 1995 and was too tight between June 1998 and August 1999. JEL Classification: E42, E52
The lack of close binaries among hot horizontal branch stars in NGC 6752

Aims. We present the results of a spectroscopic search for close binaries among horizontal branch (HB) stars in NGC 6752. Methods. We used the ESO VLT-FORS2 instrument to obtain medium resolution (R = 4100) spectra of 51 hot HB stars with 8000 K ≤ Teff ≤ 32 000 K during four consecutive nights. Eighteen of our targets are extreme horizontal branch (EHB) stars with Teff ≥ 22 000 K. Radial velocity variations were measured with cross-correlation techniques, previously evaluated the statistical and systematic errors associated with them. Results. No close binary system has been detected among our 51 targets. The data corrected for instrumental effects indicate that the radial velocity variations are always below ≈15 km s −1 (3σ level). From a statistical analysis of our results, we conclude that (at 95% confidence
Pseudomonas aeruginosa Enhances Production of a Non-Alginate Exopolysaccharide during Long-Term Colonization of the Cystic Fibrosis Lung

The gram-negative opportunistic pathogen Pseudomonas aeruginosa is the primary cause of chronic respiratory infections in individuals with the heritable disease cystic fibrosis (CF). These infections can last for decades, during which time P. aeruginosa has been proposed to acquire beneficial traits via adaptive evolution. Because CF lacks an animal model that can acquire chronic P. aeruginosa infections, identifying genes important for long-term in vivo fitness remains difficult. However, since clonal, chronological samples can be obtained from chronically infected individuals, traits undergoing adaptive evolution can be identified. Recently we identified 24 P. aeruginosa gene expression traits undergoing parallel evolution in vivo in multiple individuals, suggesting they are beneficial to the bacterium. The goal of this study was to determine if these genes impact P. aeruginosa phenotypes important for survival in the CF lung. By using a gain-of-function genetic screen, we found that 4 genes and 2 operons undergoing parallel evolution in vivo promote P. aeruginosa biofilm formation. These genes/operons promote biofilm formation by increasing levels of the non-alginate exopolysaccharide Psl. One of these genes, phaF, enhances Psl production via a post-transcriptional mechanism, while the other 5 genes/operons do not act on either psl transcription or translation. Together, these data demonstrate that P. aeruginosa has evolved at least two pathways to over-produce a non-alginate exopolysaccharide during long-term colonization of the CF lung. More broadly, this approach allowed us to attribute a biological significance to genes with unknown function, demonstrating the power of using evolution as a guide for targeted genetic studies.
Iris Recognition Based on Local Feature Point Matching

Recently, iris recognition has been paid more attention due to its high reliability in personal identification. But iris feature extraction is easily affected by some practical factors, such as inaccurate localization, occlusion, nonlinear elastic deformation and so on. In order to solve the problem, this paper presents an efficient algorithm of iris feature extraction based on scale invariant feature transform (SIFT). Experimental results show that the proposed algorithm can reduce iris preprocessing, describe iris local properties effectively and have encouraging iris recognition performance
Compressed Sensing for Accelerated EAP Recovery in Diffusion MRI

Compressed Sensing (CS) or Compressive Sampling is a recent technique to accurately reconstruct sparse signals from under sampled measurements acquired below the Shannon-Nyquist rate. In this article, we present a CS based method for accelerating the reconstruction of the Ensemble Average Propagator (EAP), also known as the Propagator in Diffusion MRI (dMRI), by significantly reducing the number of measurements. Contrarily to the time consuming acquisition technique known as the Diffusion Spectrum Imaging (DSI), our method is developed and implemented to efficiently reconstruct the EAP from reduced and non uniformly under sampled Diffusion Weighted (DW) MRI images combined to an efficient and accurate l1 norm based reconstruction algorithm. We illustrate in detail the artifacts occurring in a classical EAP reconstruction a la DSI, and qualitatively and quantitatively demonstrate good and better results in recovering the EAP and some of its important features such as the Orientation Distribution Function ( ODF) from non-regularly undersampled and l1 norm based reconstructed data. This opens an original and very interesting road to shorten the dMRI acquisition time and opens new opportunities to render High Angular Resolution Diffusion Imaging (HARDI) feasible in a clinical setting.
TDTool: threshold derivation tool

Software metrics provide basic means to quantify quality of software systems. However, the effectiveness of the measurement process is directly dependent on the definition of reliable thresholds. If thresholds are not properly defined, it is difficult to know, for instance, whether a given metric value indicates a potential problem in a class implementation. There are several methods proposed in literature to derive thresholds for software metrics. However, most of these methods (i) do not respect the skewed distribution of software metrics and (ii) do not provide a supporting tool. Aiming to fill the second gap, we propose a tool, called TDTool, to derive metric thresholds. TDTool is open source and supports four different methods for threshold derivation. This paper presents TDTool architecture and illustrates how to use it. It also presents the thresholds derived using each method based on a benchmark of 33 software product lines.
A new charge pump without degradation in threshold voltage due to body effect [memory applications]

A new charge-pump circuit with the controllable body voltage is proposed. By adjusting the body voltage, the back bias effect is removed and the threshold voltage of the MOSFET used as a switch is kept constant. With no threshold voltage increase, higher output voltage than the conventional charge pump can be obtained in the proposed charge pump. With two auxiliary MOSFETs used to update the body voltage, the proposed charge pump shows compatible performance of the ideal diode charge pump.
The Maximum Surveillance Society: The Rise of CCTV

The use of Closed-Circuit Television, or CCTV, has dramatically increased over the past decade, but its presence is often so subtle as to go unnoticed. Should we unthinkingly accept that increased surveillance is in the public's best interests, or does this mean that 'Big Brother' is finally watching us? This book asks provocative questions about the rise of the maximum surveillance society. Is crime control the principal motivation behind increased surveillance or are the reasons more complex? Does surveillance violate peoples' right of privacy? Who gets surveilled and why? What are its implications for social control? Does surveillance actually reduce crime? What will developments in technology mean for the future of surveillance? What rights do individuals under surveillance have? How is the information gathered through CCTV used by the authorities? Based on extensive fieldwork on automated surveillance in Britain over a two-year period, this book not only attempts to answer these vexing questions, but also provides a wealth of detailed information about the reasoning behind and effects of social control.
Highly Integrated Switched Beamformer Module for 2.4-GHz Wireless Transceiver Application

In this paper, a miniature switched beamformer module for 2.4-GHz applications is proposed. The proposed beamformer module is based on the integrated passive device technology, and it integrates a 4 × 4 Butler matrix, a single-pole four-throw beam-selection switch, and a p-i-n diode-based transmit/receive (T/R) switch into a compact module size of only 4.9 mm x 5 mm × 0.9 mm. To achieve the compact module size, bridged-T coils are used to replace the transmission line sections in the 4 × 4 Butler matrix and the T/R switch. The measured insertion loss at the center frequency of 2.4 GHz is within 10.89 ± 1.13 dB for the receive path and 11.33 ± 0.69 dB for the transmit path. The measured phase error is less than 8.4° at 2.4 GHz. The proposed beamformer features low cost, compact size, and low profile. It can help enable the use of phased array technique in handheld mobile devices.
Vitamin D Supplementation and Breast Cancer Prevention: A Systematic Review and Meta-Analysis of Randomized Clinical Trials

In recent years, the scientific evidence linking vitamin D status or supplementation to breast cancer has grown notably. To investigate the role of vitamin D supplementation on breast cancer incidence, we conducted a systematic review and meta-analysis of randomized controlled trials comparing vitamin D with placebo or no treatment. We used OVID to search MEDLINE (R), EMBASE and CENTRAL until April 2012. We screened the reference lists of included studies and used the “Related Article” feature in PubMed to identify additional articles. No language restrictions were applied. Two reviewers independently extracted data on methodological quality, participants, intervention, comparison and outcomes. Risk Ratios and 95% Confident Intervals for breast cancer were pooled using a random-effects model. Heterogeneity was assessed using the I2 test. In sensitivity analysis, we assessed the impact of vitamin D dosage and mode of administration on treatment effects. Only two randomized controlled trials fulfilled the pre-set inclusion criteria. The pooled analysis included 5372 postmenopausal women. Overall, Risk Ratios and 95% Confident Intervals were 1.11 and 0.74–1.68. We found no evidence of heterogeneity. Neither vitamin D dosage nor mode of administration significantly affected breast cancer risk. However, treatment efficacy was somewhat greater when vitamin D was administered at the highest dosage and in combination with calcium (Risk Ratio 0.58, 95% Confident Interval 0.23–1.47 and Risk Ratio 0.93, 95% Confident Interval 0.54–1.60, respectively). In conclusions, vitamin D use seems not to be associated with a reduced risk of breast cancer development in postmenopausal women. However, the available evidence is still limited and inadequate to draw firm conclusions. Study protocol code: FARM8L2B5L.
Formal Modeling for Multi-Level Authentication in Sensor-Cloud Integration System

Recent developments in sensor networking emphasized the need for integration of sensor networks with the cloud. This improves the processing power and battery life of the sensor nodes. Once the sensor data is routed to the cloud, possible measures need to be adopted to secure the sensor data. Thus, strict authentication checks have to be provided to facilitate authorized customers to utilize the services provided by the cloud in the form of sensor data. In this paper, we present an authentication system by employing the multi-level authentication technique in securing the sensor data in cloud. This technique generates/authenticates the password in multiple levels to access cloud services. Thus, the proposed scheme helps in improving the authentication level by order of magnitude as compared to the existing technique. We modeled the proposed system using Petri nets. General Terms Cloud Computing, Sensor Network, Security
Corrections to "General Scheme of Region Competition Based on Scale Space"

ÐIn this paper, we propose a general scheme of region competition (GSRC) for image segmentation based on scale space. First, we present a novel classification algorithm to cluster the image feature data according to the generally defined peaks under a certain scale and a scale space-based classification scheme to classify the pixels by grouping the resultant feature data clusters into several classes with a standard classification algorithm. Second, to reduce the resultant segmentation error, we develop a nonparametric probability model from which the functional for GSRC is derived. Third, we design a general and formal approach to automatically determine the initial regions. Finally, we propose the kernel procedure of GSRC which segments an image by minimizing the functional. The strategy adopted by GSRC is first to label pixels whose corresponding regions can be determined in large likelihood, and then to fine-tune the final regions with the help of the nonparametric probability model, boundary smoothing, and region competition. GSRC quantitatively controls the segmentation extent with the scale space-based classification scheme. Although the description of the scheme is nonparametric in this paper, GSRC can also work parametrically if all nonparametric procedures in this paper are substituted with the parametric counterparts. Index TermsÐNonparametric probability model, region competition, region growing, scale space-based classification, segmentation.
A Unified Framework for Instruction Scheduling and Mapping for Function Units with Structural Hazards

Software pipelining methods based on an ILP (integer linear programming) framework have been successfully applied to derive rate-optimal schedules under resource constraints. However, like many other previous works on software pipelining, ILP-based work has focused on resource constraints of simple function units, e.g., “clean pipelines”? pipelines without structural hazards. The problem for architectures beyond such clean pipelines remains open. One challenge is how to represent such resource constraints for unclean pipelines, i.e., pipelined function units, but having structural hazards.In this paper, we propose a method to constructrate-optimalsoftware pipelined schedules for pipelined architectures with structural hazards. A distinct feature of this work is that it provides a unified ILP framework for two challenging and interrelated aspects of software pipelining? the scheduling of instructions at particular times and the mapping of those instructions to specific function units. Solving both of these aspects is essential to finding schedules which will work both on VLIW machines which map instructions to fixed function units and on dynamic out-of-order superscalars. We propose two ILP formulations to solve the integrated scheduling and mapping problem. Both adopt principles of graph coloring in an ILP framework, and one usesforbidden latenciesin an elegant extension of classical hardware pipeline control theory.We have run experiments on four variations of our proposed formulations. As input we used a set of 415 “unique” loops taken from several benchmark suites, and we targeted an architecture whose function units contain many structural hazards. All four of our variations did well, with the best finding a rate-optimal schedule for 65% of the loops. This compares favorably with a leading heuristic, Huff'sSlack Scheduling? the ILP approaches found a schedule with smaller initiation interval for over 50% of the loops, with a mean improvement of almost 30%. Finally, we have found that reusing pipeline stages? and thus adding hazards? results in only a 10% drop in performance, while permitting significant savings in area.