Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Damage Complexity-Dependent Non-Homologous End-Joining Repair Pathway

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several repair proteins such as Ku, DNA-PKcs, and XRCC4. It has been experimentally shown that the choice of NHEJ proteins is determined by the complexity of DSB. In this paper, we built a mathematical model, based on published data, to study how NHEJ depends on the damage complexity. Under an appropriate set of parameters obtained by minimization technique, we can simulate the kinetics of foci track formation in fluorescently tagged mammalian cells, Ku80-EGFP and DNA-PKcs-YFP for simple and complex DSB repair, respectively, in good agreement with the published experimental data, supporting the notion that simple DSB undergo fast repair in a Ku-dependent, DNA-PKcs-independent manner, while complex DSB repair requires additional DNA-PKcs for end processing, resulting in its slow repair, additionally resulting in slower release rate of Ku and the joining rate of complex DNA ends. Based on the numerous experimental descriptions, we investigated several models to describe the kinetics for complex DSB repair. An important prediction of our model is that the rejoining of complex DSBs is through a process of synapsis formation, similar to a second order reaction between ends, rather than first order break filling/joining. The synapsis formation (SF) model allows for diffusion of ends before the synapsis formation, which is precluded in the first order model by the rapid coupling of ends. Therefore, the SF model also predicts the higher number of chromosomal aberrations observed with high linear energy transfer (LET) radiation due to the higher proportion of complex DSBs compared to low LET radiation, and an increased probability of misrejoin following diffusion before the synapsis is formed, while the first order model does not provide a mechanism for the increased effectiveness in chromosomal aberrations observed.
Noise properties of gravitational lens mass reconstruction

Gravitational lensing is potentially able to observe mass-selected haloes, and to measure the projected cluster mass function. An optimal mass selection requires a quantitative understanding of the noise behaviour in mass maps. This paper is an analysis of the noise properties in mass maps reconstructed from a maximum-likelihood method. The first part of this work is the derivation of the noise power spectrum and the mass error bars as a straightforward extension of the Kaiser & Squires algorithm for the case of a correlated noise. Very good agreement is found between these calculations and the noise properties measured in the mass reconstructions limited to non-critical clusters of galaxies. It demonstrates that Kaiser & Squires and maximum-likelihood methods have similar noise properties and that the weak lensing approximation is valid for describing these properties. In a second stage I show that the statistics of peaks in the noise follows accurately the peak statistics of a two-dimensional Gaussian random field (using the BBKS techniques) if the smoothing aperture contains enough galaxies. This analysis provides a full procedure for deriving the significance of any convergence peak as a function of its amplitude and profile. I demonstrate that a detailed quantitative analysis of the structures in mass maps can be carried out, and that, to a very good approximation, a mass map is the sum of the lensing signal and known two-dimensional Gaussian random noise. A straightforward application is the measurement of the projected mass function in wide-field lensing surveys, down to small mass overdensities that are individually undetectable.
Root Exudation: The Ecological Driver of Hydrocarbon Rhizoremediation

Rhizoremediation is a bioremediation technique whereby microbial degradation of organic contaminants occurs in the rhizosphere. It is considered to be an effective and affordable “green technology” for remediating soils contaminated with petroleum hydrocarbons. Root exudation of a wide variety of compounds (organic, amino and fatty acids, carbohydrates, vitamins, nucleotides, phenolic compounds, polysaccharides and proteins) provide better nutrient uptake for the rhizosphere microbiome. It is thought to be one of the predominant drivers of microbial communities in the rhizosphere and is therefore a potential key factor behind enhanced hydrocarbon biodegradation. Many of the genes responsible for bacterial adaptation in contaminated soil and the plant rhizosphere are carried by conjugative plasmids and transferred among bacteria. Because root exudates can stimulate gene transfer, conjugation in the rhizosphere is higher than in bulk soil. A better understanding of these phenomena could thus inform the development of techniques to manipulate the rhizosphere microbiome in ways that improve hydrocarbon bioremediation.
Dietary Fat Intake and Risk of Gastric Cancer: A Meta-Analysis of Observational Studies

Background and Objectives Consumption of dietary fat has been reported to be associated with gastric cancer risk, but the results of epidemiologic studies remain inconsistent. We conducted a meta-analysis to summarize the evidence regarding the association between dietary fat intake and gastric cancer risk. Methods A comprehensive search of PubMed and EMBASE was performed to identify observational studies providing quantitative estimates between dietary fat and gastric cancer risk. Random effects model was used to calculate the summary relative risk(SRR) in the highest versus lowest analysis. Categorical dose-response analysis was conducted to quantify the association between dietary fat intake and gastric cancer risk. Heterogeneity among studies was evaluated using I2 and tau2(between study variance)statistics. Subgroup analysis and publication bias analysis were also performed. Results Twenty-two articles were included in the meta-analysis. The SRR for gastric cancer was 1.18 for individuals with highest intake versus lowest intake of total fat (95% confidence interval [CI]: 0.999–1.39; n = 28; P< 0.001; tau2 = 0.12; I2 = 69.5%, 95% CI: 55%-79%) and 1.08 with a daily increase in total fat intake (20 g/d) (95%CI: 1.02–1.14; n = 6; P = 0.09; tau2 = 0.002; I2 = 46.8%, 95% CI: 0%-79%). Positive association between saturated fat intake (SRR = 1.31; 95%CI: 1.09–1.58;n = 18;P<0.001; tau2 = 0.08; I2 = 60.6%, 95% CI: 34%-76%), inverse association between polyunsaturated fat intake (SRR = 0.77; 95%CI: 0.65–0.92; n = 16; P = 0.003; tau2 = 0.06; I2 = 56.2%, 95% CI: 23%-75%) and vegetable fat intake (SRR = 0.55; 95%CI: 0.41–0.74; n = 4;P = 0.12; tau2 = 0.04; I2 = 48.6%, 95% CI: 0%-83%), and no association between monounsaturated fat intake (SRR = 1.00; 95%CI: 0.79–1.25; n = 14; P< 0.001; tau2 = 0.10; I2 = 63.0%, 95% CI: 34%-79%) and animal fat intake (SRR = 1.10; 95%CI: 0.90–1.33; n = 6; P = 0.13;tau2 = 0.02; I2 = 42.0%, 95% CI: 0%-70%) and gastric cancer risk were observed. Conclusions Our results suggest that intake of total fat is potentially positively associated with gastric cancer risk, and specific subtypes of fats account for different effects. However, these findings should be confirmed by further well-designed cohort studieswith detailed dietary assessments and strict control of confounders.
On the efficient memory usage in the lifting scheme for the two-dimensional wavelet transform computation

In this paper, a new algorithm to efficiently implement the two-dimensional lifting scheme is presented. The 1D lifting-scheme performs in-place processing of the input samples, and hence it provides reduction in memory requirements. However, for image processing (2D), in-place computation is not enough, resulting in a memory-intensive algorithm, since it has to keep the whole image in memory. We propose the use of line-by-line processing algorithm for the lifting scheme, and we address some issues on how to perform synchronization among different buffer levels, so that an implementation can be easily written. Experimental results show that, for a 5-megapixel image, our algorithm requires 200 times less memory and it is more than 3 times faster than the usual one.
A. Appendix A.1. Declaration of GregorianDate

Using exception handling in C++ can lead to severe problems with dynamic objects and other resources— dangling pointers, memory leaks etc. By using a small set of patterns (collected into a pattern language “Exception-safe C++ objects”), these problems can be avoided. However, it turns out that these pattern make use of “resource management”, which poses a lot of questions in itself. For the solution of these problems, a second, somewhat larger set of patterns (collected into a pattern language “Responsibility management under exception handling”) is provided.
Mono versus .net: A Comparative Study of Performance for Distributed Processing

A portable heating unit comprising a heater and a low velocity blower, an elongated lightweight collapsible flexible heat carrying duct and an intermediate high velocity intake fan unit for mixing the low velocity heated air from said portable heater with ambient air and introducing the mixed air streams into the inlet end of said flexible duct. The intake fan unit includes a venturi for assuring adequate mixing of the air within the elongated flexible collapsible tube to provide a high velocity flow of air at a substantially constant temperature level along the length of the flexible tube. The tube is provided with a plurality of openings arranged in spaced intervals to eject high velocity jets of heated air at locations where they may be used most effectively. The unit is designed to be positioned upon the ground and the remote end is sealed and preferably staked or otherwise held to the ground to prevent undue movement. The diameter of the elongated flexible tube is selected to enable the tube to fit beneath a bench, preferably made of a metallic material to provide good heat conductivity. Openings are provided in the tube to emit air beneath the bench in order to heat the bench and thereby provide much needed warmth to persons sitting on the bench. Additional openings are arranged to emit the heated air at an angle chosen to direct the air toward the back part of the knees of persons sitting upon the bench. High velocity jets of heated air emitted from such openings may also be utilized as handwarming means for simultaneously warming the hands of a large group of persons in the vicinity of the tube by placement of the hands into the jets of heated air being emitted by said tube without danger of burning. The lightweight collapsible nature of the apparatus greatly facilitate both assembly and disassembly as well as the transportability of the portable heating system.
Economic impacts of agricultural research and extension

Agricultural research and extension programs have been built in most of the world's economies. A substantial number of economic impact studies evaluating the contributions of research and extension programs to increased farm productivity and farm incomes and to consumer welfare have been undertaken in recent years. This chapter reviews these studies using estimated rates of return on investment to index economic impacts. In almost all categories of studies, median (social) estimated rates of return are high, (often exceeding 40 percent) but the range of estimates was also high. The chapter concludes that most of the estimates were consistent with actual economic growth experiences.
The HIV-1 Reverse Transcriptase M184I Mutation Enhances the E138K-Associated Resistance to Rilpivirine and Decreases Viral Fitness

BackgroundThe registrational phase III clinical trials of the nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) rilpivirine (RPV) in combination with two nucleoside/nucleotide RT inhibitors (NRTIs) found a unique genotypic resistance pattern involving the NNRTI mutation E138K with the NRTI mutation M184I. Eighty percent of subjects used emtricitabine (FTC) and tenofovir disoproxil fumarate (TDF); a single tablet regimen of FTC/RPV/TDF is in development. MethodsHIV-1 with E138K and/or M184V or I mutations were constructed and phenotyped in MT-2 cells and the PhenoSense and Antivirogram assays. Viral fitness was determined using growth competitions. Molecular models of the mutants were constructed from the RT-RPV crystal structure. ResultsThe E138K mutant showed low-level reduced susceptibility to RPV (2.4-fold), but full susceptibility to FTC and tenofovir (TFV). Viruses with M184V or M184I showed high-level resistance to FTC and full susceptibility to RPV and TFV. Addition of M184I, but not M184V, to E138K, further decreased susceptibility to RPV and maintained FTC resistance. The E138K and M184V or I single and double mutants showed decreased replication fitness compared with wild type. M184V outcompeted M184I when compared directly and in the background of E138K. E138K + M184I was less fit than either E138K or M184I alone. Removing a salt bridge between E138/K101 is implicated in resistance to RPV. ConclusionsThe higher frequency of E138K and M184I among RPV + FTC/TDF virologic failures is due to reduced susceptibility of the single mutants to RPV and FTC and the enhanced resistance to RPV for the double mutant at the cost of decreased viral fitness.
A Simple Critical-Load-Based CAC Scheme for IEEE 802.11 DCF Networks

This paper proposes a simple and practical call admission control (CAC) scheme for one-hop IEEE 802.11 distributed coordination function (DCF) networks in heterogeneous environments. The proposed scheme is the first CAC scheme derived from an asymptotic analysis of the critical traffic load, where the critical traffic load represents the threshold for queue stability. The salient feature of our CAC scheme is that it can be performed quickly and easily without the need for network performance measurements and complex calculations. Using the proposed scheme, we specifically investigate the voice capacity of 802.11 DCF networks with unbalanced traffic. Extensive simulations covering both ad hoc and infrastructure-based networks, and a variety of nonsaturated traffic types, show that the proposed CAC scheme is very effective.
Standards-Based Leadership: A Case Study Book for the Principalship

Today's school principal is charged with the responsibility for creating a learning organization which emphasizes success for all students. An important component leading to these successful school experiences is decision-making based on standards that are grounded in research and best-practice. Standards-Based Leadership: A Case Study Book for the Principalship provides a structure for learning and growth that connects theory with practice whether the principal is already 'on the job' or enrolled in a preparation program. Each chapter is organized around identification of a major ELCC standard, as well as the Texas standards. The scenarios are all based on real problems that have faced real principals. Applying the descriptors of the standard and using the brief literature reviews as resources to guide decision-making, principals are provided with a framework for implementation of specific strategies that will best help students. As school leaders reflect on the realistic situations provided in each chapter and identify possible applications and implications, they will be strengthened in their quest to meet the challenges of standards-based leadership for the principalship.
Adaptive Feature Ranking for Unsupervised Transfer Learning

Transfer Learning is concerned with the application of knowledge gained from solving a problem to a different but related problem domain. In this paper, we propose a method and efficient algorithm for ranking and selecting representations from a Restricted Boltzmann Machine trained on a source domain to be transferred onto a target domain. Experiments carried out using the MNIST, ICDAR and TiCC image datasets show that the proposed adaptive feature ranking and transfer learning method offers statistically significant improvements on the training of RBMs. Our method is general in that the knowledge chosen by the ranking function does not depend on its relation to any specific target domain, and it works with unsupervised learning and knowledge-based transfer.
Mining Information of Anonymous User on a Social Network Service

The growing number of individuals is recently writing their own opinions or information freely at the network space on the web such as the blog or Online Cafe and these network spaces are developed toward a new service called social network. Consequently, a lot of researchers are studying this social network lively. The social network is not only a tool for providing real time news, but also having an effect on an opinion or a policy decision. It uses mainly texts to present information in real-time, and its users use a computer or a mobile device to upload their own opinions or ideas. A lot of texts from users contain important and various information. We will get this information we need real-time if semantic can be extracted from texts on a social network. In this case, Opinion mining should be useful to extract semantic from social network. This paper suggests a noble method to grasp information of anonymous users through relationship information available and their psychology that is reflected on texts and also understand the meanings of contents in depth.
Workers and Welfare

After the revolutionary period of 1910-1920, Mexico developed a number of social protection programs to support workers in public and private sectors and to establish safeguards for the poor and the aged. These included pensions, healthcare, and worker's compensation. The new welfare programs were the product of a complex interrelationship of corporate, labor, and political actors. In this unique dynamic, cross-class coalitions maintained both an authoritarian regime and social protection system for some seventy years, despite the ebb and flow of political and economic tides. By focusing on organized labor, and its powerful role in effecting institutional change, "Workers and Welfare" chronicles the development and evolution of Mexican social insurance institutions in the twentieth century. Beginning with the antecedents of social insurance and the adoption of pension programs for central government workers in 1925, Dion's analysis shows how the labor movement, up until the 1990s, was instrumental in expanding welfare programs, but has since become largely ineffective. Despite stepped-up efforts, labor has seen the retrenchment of many benefits. Meanwhile, Dion cites the debt crisis, neoliberal reform, and resulting changes in the labor market as all contributing to a rise in poverty. Today, Mexican welfare programs emphasize poverty alleviation, in a marked shift away from social insurance benefits for the working class.
International Journal of Advanced Robotic Systems Spatial Programming for Industrial Robots Through Task Demonstration Regular Paper

We present an intuitive system for the programming of industrial robots using markerless gesture recognition and mobile augmented reality in terms of programming by demonstration. The approach covers gesture‐based task definition and adaption by human demonstration, as well as task evaluation through augmented reality. A 3D motion tracking system and a handheld device establish the basis for the presented spatial programming system. In this publication, we present a prototype toward the programming of an assembly sequence consisting of several pick‐and‐place tasks. A scene reconstruction provides pose estimation of known objects with the help of the 2D camera of the handheld. Therefore, the programmer is able to define the program through natural bare‐hand manipulation of these objects with the help of direct visual feedback in the augmented reality application. The program can be adapted by gestures and transmitted subsequently to an arbitrary industrial robot controller using a unified interface. Finally, we discuss an application of the presented spatial programming approach toward robot‐based welding tasks.
A randomized, phase II trial of cetuximab with or without PX-866, an irreversible oral phosphatidylinositol 3-kinase inhibitor, in patients with relapsed or metastatic head and neck squamous cell cancer.

BACKGROUND The phosphotidylinositol-3 kinase (PI3K)/serine-threonine kinase/mammalian target of rapamycin signaling pathway is frequently altered in head and neck squamous cell cancer (HNSCC). PX-866 is an oral, irreversible, pan-isoform inhibitor of PI3K. A phase I trial demonstrated tolerability of this combination. This randomized phase II study evaluated PX-866 combined with cetuximab in patients with advanced, refractory HNSCC. METHODS Patients with recurrent or metastatic HNSCC who had received at least one and no more than two prior systemic treatment regimens were randomized (1 : 1) to cetuximab with or without PX-866 (8 mg p.o. daily; arms A and B, respectively). The primary end point was progression-free survival (PFS). Secondary end points included objective response rate (ORR), overall survival (OS), toxicity, and correlation of key biomarkers with efficacy outcomes. RESULTS Eighty-three patients were enrolled. There was a similar response rate between arms (10% versus 7%). Of patients for whom tissue was assessable, 57% were human papillomavirus (HPV) positive. Median PFS was 80 days in both arms and there was no difference in OS between the two arms (211 versus 256 days). Overall toxicity was higher in arm A compared with arm B, especially in terms of nausea (53% versus 23%), vomiting (45% versus 15%), fatigue (43% versus 23%), diarrhea (40% versus 21%), and hypokalemia (25% versus 10%). Grade 3 or higher adverse events were infrequent, but more common in the combination arm although without a specific pattern. PIK3CA mutations were observed in 17% of the cases assessed, and PTEN loss was infrequently observed. CONCLUSION The addition of PX-866 to cetuximab did not improve PFS, RR, or OS in patients with advanced, refractory HNSCC enrolled without molecular preselection. In this contemporary cohort, HPV-positive patients comprised the majority, and neither HPV-positive nor HPV-negative patients derived clinical benefit for the addition of cetuximab plus PX-866.