Miracle-dz/UniFAR-FTUs huggingface dataset:
LuxArray, a High-Density, Genomewide Transcription Analysis of Escherichia coli Using Bioluminescent Reporter Strains

ABSTRACT A sequenced collection of plasmid-borne random fusions ofEscherichia coli DNA to a Photorhabdus luminescens luxCDABE reporter was used as a starting point to select a set of 689 nonredundant functional gene fusions. This group, called LuxArray 1.0, represented 27% of the predicted transcriptional units in E. coli. High-density printing of the LuxArray 1.0 reporter strains to membranes on agar plates was used for simultaneous reporter gene assays of gene expression. The cellular response to nalidixic acid perturbation was analyzed using this format. As expected, fusions to promoters of LexA-controlled SOS-responsive genes dinG, dinB, uvrA, and ydjM were found to be upregulated in the presence of nalidixic acid. In addition, six fusions to genes not previously known to be induced by nalidixic acid were also reproducibly upregulated. The responses of two of these, fusions to oraA andyigN, were induced in a LexA-dependent manner by both nalidixic acid and mitomycin C, identifying these as members of the LexA regulon. The responses of the other four were neither induced by mitomycin C nor dependent on lexA function. Thus, the promoters of ycgH, intG, rihC, and a putative operon consisting of lpxA, lpxB, rnhB,and dnaE were not generally DNA damage responsive and represent a more specific response to nalidixic acid. These results demonstrate that cellular arrays of reporter gene fusions are an important alternative to DNA arrays for genomewide transcriptional analyses.
A New Generic Algorithm for Scalar Multiplication

In this paper, we present a generic algorithm for evaluating the multiple of a point on an elliptic curve;or more generally, for computing an exponentiation in arbitrary Abelian group. Our algorithm uses a ternary representation for scalars and achieves both fast performance and resistivity against SPA attacks and safe error attacks. Moreover, our algorithm nicely works in parallel. Comparisons show that our proposed algorithm establishes a faster scalar multiplication. The most important observation is that our proposed algorithm makes greater improvements for Hessian form curve over fields of characteristic three than any other curves overlarge prime fields or binary fields.
Explorer Exome Sequencing : Current and Future Perspectives

The falling cost of DNA sequencing has made the technology affordable to many research groups, enabling researchers to link genomic variants to observed phenotypes in a range of species. This review focusses on whole exome sequencing and its applications in humans and other species. The exome has traditionally been defined to consist of only the protein coding portion of the genome; a region where mutations are likely to affect protein structure and function. There are several commercial kits available for exome sequencing in a number of species and, owing to the highly conserved nature of exons, many of these can be applied to other closely related species. The data set produced from exome sequencing is many times smaller than that of whole genome sequencing, making it more easily manageable and the analysis less complex. Exome sequencing for disease gene discovery in humans is well established and has been used successfully to identify mutations that are causative of complex and rare diseases. Exome sequencing has also been used in a number of domesticated and companion species. The successful application of exome sequencing to crops has yielded results that may be used in selective breeding to improve production in these species, and there is potential for exome sequencing to provide similar advances in livestock species that have not yet been realised.
Methodological approaches to determining the marine radiocarbon reservoir effect

The marine radiocarbon reservoir effect is an offset in 14C age between contemporaneous organisms from the terrestrial environment and organisms that derive their carbon from the marine environment. Quantification of this effect is of crucial importance for correct calibration of the 14C ages of marine-influenced samples to the calendrical timescale. This is fundamental to the construction of archaeological and palaeoenvironmental chronologies when such samples are employed in 14C analysis. Quantitative measurements of temporal variations in regional marine reservoir ages also have the potential to be used as a measure of process changes within Earth surface systems, due to their link with climatic and oceanic changes. The various approaches to quantification of the marine radiocarbon reservoir effect are assessed, focusing particularly on the North Atlantic Ocean. Currently, the global average marine reservoir age of surface waters, R(t), is c. 400 radiocarbon years; however, regional values deviate from this as a function of climate and oceanic circulation systems. These local deviations from R(t) are expressed as +R values. Hence, polar waters exhibit greater reservoir ages (δR = c. +400 to +800 14C y) than equatorial waters (δR = c. 0 14C y). Observed temporal variations in δR appear to reflect climatic and oceanographic changes. We assess three approaches to quantification of marine reservoir effects using known age samples (from museum collections), tephra isochrones (present onshore/offshore) and paired marine/terrestrial samples (from the same context in, for example, archaeological sites). The strengths and limitations of these approaches are evaluated using examples from the North Atlantic region. It is proposed that, with a suitable protocol, accelerator mass spectrometry (AMS) measurements on paired, short-lived, single entity marine and terrestrial samples from archaeological deposits is the most promising approach to constraining changes over at least the last 5 ky BP.
Denoising of Hyperspectral Images Using Group Low-Rank Representation

Hyperspectral images (HSIs) have been used in a wide range of fields, such as agriculture, food safety, mineralogy, and environment monitoring, but being corrupted by various kinds of noise limits its efficacy. Low-rank representation (LRR) has proved its effectiveness in the denoising of HSIs. However, it just employs local information for denoising, which results in ineffectiveness when local noise is heavy. In this paper, we propose an approach of group low-rank representation (GLRR) for the HSI denoising. In our GLRR, a corrupted HSI is divided into overlapping patches, the similar patches are combined into a group, and the group is reconstructed as a whole using LRR. The proposed method enables the exploitation of both the local similarity within a patch and the nonlocal similarity across the patches in a group simultaneously. The additional nonlocally similar patches can bring in extra structural information to the corrupted patches, facilitating the detection of noise as outliers. LRR is applied to the group of patches, as the uncorrupted patches enjoy intrinsic low-rank structure. The effectiveness of the proposed GLRR method is demonstrated qualitatively and quantitatively by using both simulated and real-world data in experiments.
Efficient dynamic minimization of word-level DDs based on lower bound computation

Word-Level Decision Diagrams (WLDDs), like *BMDs or K*BMDs, have been introduced to overcome the limitations of Binary Decision Diagrams (BDDs), which are the state-of-the-art data structure to represent and manipulate Boolean functions. However, the size of these graph types largely depends on the variable ordering, i.e. it may vary from linear to exponential. In the meantime, dynamic approaches to find a good variable ordering are also known for WLDDs. In this paper we show how these approaches can be accelerated significantly using a combination of a lower bound computation and synthesis operations. In the experiments it turned out that by this technique, the runtime for dynamic minimization can be reduced by more than 40% on average without loss of quality.
A Comparative Study of Proposed Genetic Algorithm-Based Solution with Other Algorithms for Time-Dependent Vehicle Routing Problem with Time Windows for E-Commerce Supply Chain

The vehicle routing problem (VRP) is classified as an NP-hard problem. Hence exact optimization methods may be difficult to solve these problems in acceptable CPU times, when the problem involves real-world data sets that are very large. To get solutions in determining routes which are realistic and very close to the optimal solution, one has to use heuristics and meta-heuristics. In this paper, an attempt has been made to develop a GA based meta-heuristic to solve the time dependent vehicle route problem with time windows (TDVRPTW). This algorithm is compared with five other existing algorithms in terms of minimizing the number of vehicles used as well as the total distance travelled. The algorithms are implemented using Matlab and HeuristicLab optimization software. A plugin was developed using Visual C# and NET Framework 4.5. Results were tested using Solomon’s 56 benchmark instances (of which 24 instances are used with 4 in each of the 6 problem classes) classified into groups such as C1, C2, R1, R2, RC1, and RC2. For each of the performance measures, through a complete factorial experiment with two factors, it is proved that the proposed algorithm is the best among all the six algorithms compared in this paper.
View Selection in DW and OLAP: A Theoretical Review

Data Warehousing (DW) systems store materialized views, data marts and data cubes, and provide nicely data exploration and analysis interfaces via OnLine Analytical Processing (OLAP) (Gray et al., 1997) and Data Mining (DM) tools and algorithms. Also, OnLine Analytical Mining (OLAM) (Han, 1997) integrates the previous knowledge discovery methodologies and offers a meaningfully convergence between OLAP and DM, thus contributing to significantly augment the power of data exploration and analysis capabilities of knowledge workers. At the storage layer, the mentioned knowledge discovery methodologies share the problem of efficiently accessing, querying and processing multidimensional data, which in turn heavily affect the performance of knowledge discovery processes at the application layer. Due to the fact that OLAP and OLAM directly process data cubes/marts, and DM is more and more encompassing methodologies that are interested to multidimensional data, the problem of efficiently representing data cubes by means of a meaningfully selected view set is become of relevant interest for the Data Warehousing and OLAP research community. This problem is directly related to the analogous problem of efficiently computing the data cube from a given relational data source (Harinarayan et al., 1996; Agarwal et al., 1996; Sarawagi et al., 1996; Zhao et al., 1997). Given a relational data source R and a target data cube schema W, the view selection problem in OLAP deals with how to select and materialize views from R in order to compute the data cube A defined by the schema W by optimizing both the query processing time, denoted by TQ, which models the amount of time required to answer a reference query-workload on the materialized view set, and the view maintenance time, denoted by TM, which models the amount of time required to maintain the materialized view set when updates occur, under a given set of constraints I that, without any loss of generality, can be represented by a space bound constraint B limiting the overall occupancy of the views to be materialized (i.e., I = 〈B〉). It has been demonstrated (Gupta, 1997; Gupta & Mumick, 2005) that this problem is NP-hard, thus heuristic schemes are necessary. Heuristics are, in turn, implemented in the vest of greedy algorithms (Yang et al., 1997; Kalnis et al., 2002). In this article, we focus the attention on state-ofthe-art methods for the view selection problem in Data Warehousing and OLAP, and complete our analytical contribution with a theoretical analysis of these proposals under different selected properties that nicely model spatial and temporal complexity aspects of the investigated problem.
Establishing trust in black-box programs

Encrypted binaries are increasingly being used as deterrence for software piracy as well as vulnerability exploitation. The application of encrypted programs, however, leads to increased security concerns, as users are unable to identify malicious behavior by monitoring the encrypted executables. This paper proposes a method to monitor encrypted programs that assures users that the black-box program on their system is not violating any security concerns. Our approach is to embed a system call monitoring tool into the operating system that monitors system call content for suspicious behavior or the lack thereof.
Joint Optimization of Transmit Power and Codebook Size for Multiuser MISO Systems

Transmit power and feedback bandwidth are two limited and interrelated resources which are crucial to system performance in wireless channel with feedback, so it is necessary to maximize their utilization efficiencies in the joint sense. In this paper, we investigate the inherent relationship between transmit power and codebook size in multiuser limited feedback MISO system by making use of Grassmann line packing theory, as an effort to provide an insight on how to jointly distribute the two resources to fulfill the diverse requirements. Then, the impact of feedback delay on the tradeoff relation is characterized in detail, and we find that even with relatively small delay, there is considerable performance loss with respect to the ideal case. Thereby, much more transmit power or feedback bandwidth should be consumed to achieve the same performance target. Finally, the theoretical claims are validated by numerical results.
A sub-2W 39.8-to-44.6Gb/s transmitter and receiver chipset with SFI-5.2 interface in 40nm CMOS

The introduction of 40Gb/s networks, spurred by 40Gb/s WDM growth, can alleviate bandwidth bottlenecks of Internet infrastructure while simultaneously reducing operating costs. Increasingly, standard CMOS technology is used to enable transceiver speeds [1-5] previously achievable only by using expensive bipolar technology. However, at 40Gb/s, limited channel bandwidth coupled with stringent receiver jitter tolerance requirements demands better solutions than exist currently.
Band Instrument Selection and Assignment

This review of the literature examines the process of matching students with band instruments as presented in academic research journals and practitioner publications. While some directors may evaluate the potential impact of students’ physical characteristics such as lip size and shape, teeth and jaw structure, body build, and so forth, other sources have cited the importance of fine- and gross-motor coordination, aural skills acuity, music aptitude, timbre preference, motivation, personality, and environmental influences. A few empirical studies have suggested a positive impact on student achievement and retention when professional educators assist students in selecting instruments. Despite conflicting information, helping students match their gifts to specific instruments deserves careful study and more attention from those who assist students in selecting instruments. Motivation to play a particular instrument is a strong factor in predicting success and persistence. Some suggestions for possible approaches to clear up some of the ambiguity are provided.
Ecological Foundations for Fire Management in North American Forest and Shrubland Ecosystems

This synthesis provides an ecological foundation for management of the diverse ecosystems and fire regimes of North America, based on scientific principles of fire interactions with vegetation, fuels, and biophysical processes. Although a large amount of scientific data on fire exists, most of those data have been collected at small spatial and temporal scales. Thus, it is challenging to develop consistent science-based plans for large spatial and temporal scales where most fire management and planning occur. Understanding the regional geographic context of fire regimes is critical for developing appropriate and sustainable management strategies and policy. The degree to which human intervention has modified fire frequency, intensity, and severity varies greatly among different ecosystems, and must be considered when planning to alter fuel loads or implement restorative treatments. Detailed discussion of six ecosystems—ponderosa pine forest (western North America), chaparral (California), boreal forest (Alaska and Canada), Great Basin sagebrush (intermountain West), pine and pine-hardwood forests (Southern Appalachian Mountains), and longleaf pine (Southeastern United States)— illustrates the complexity of fire regimes and that fire management requires a clear regional focus that recognizes where conflicts might exist between fire hazard reduction and resource needs. In some systems, such as ponderosa pine, treatments are usually compatible with both fuel reduction and resource needs, whereas in others, such as chaparral, the potential exists for conflicts that need to be closely evaluated. Managing fire regimes in a changing climate and social environment requires a strong scientific basis for developing fire management and policy.
The TREC-8 Question Answering Track Evaluation

The TREC-8 Question Answering track was the (cid:12)rst large-scale evaluation of systems that return answers, as opposed to lists of documents, in response to a question. As a (cid:12)rst evaluation, it is important to examine the evaluation methodology itself to understand any limits on the conclusions that can be drawn from the evaluation and possibly to (cid:12)nd ways to improve subsequent evaluations. This paper has two main goals: to describe in detail how the evaluation was implemented, and to examine the consequences of the methodology on the comparative performance of the systems participating in the evaluation. The examination uncovered no serious (cid:13)aws in the methodology, supporting its continued use for question answering evaluation. Nonetheless, rede(cid:12)ning the speci(cid:12)c task to be performed so that it more closely matches an actual user task does appear warranted
Nonorthogonal locally one dimensional FDTD method

We present unconditionally stable Non-orthogonal Locally One Dimensional (LOD) finite-difference time-domain (FDTD) method. The non-orthogonal formulation can be useful to extend the LOD-FDTD methods for curved discontinuities so as to obtain more accurate results with reduced computational resources. Formulations for CPML as well as scattered-field formulation are provided. Numerical simulations are used to demonstrate the accuracy and improvement of the proposed method over the conventional and non-orthogonal FDTD algorithms.
Subglacial discharge at tidewater glaciers revealed by seismic tremor

Subglacial discharge influences glacier basal motion and erodes and redeposits sediment. At tidewater glacier termini, discharge drives submarine terminus melting, affects fjord circulation, and is a central component of proglacial marine ecosystems. However, our present inability to track subglacial discharge and its variability significantly hinders our understanding of these processes. Here we report observations of hourly to seasonal variations in 1.5–10 Hz seismic tremor that strongly correlate with subglacial discharge but not with basal motion, weather, or discrete icequakes. Our data demonstrate that vigorous discharge occurs from tidewater glaciers during summer, in spite of fast basal motion that could limit the formation of subglacial conduits, and then abates during winter. Furthermore, tremor observations and a melt model demonstrate that drainage efficiency of tidewater glaciers evolves seasonally. Glaciohydraulic tremor provides a means by which to quantify subglacial discharge variations and offers a promising window into otherwise obscured glacierized environments.
Pancreatic Enzymes and Microvascular Cell Activation in Multiorgan Failure

Cell activation in the microcirculation leads to an inflammatory cascade and is accompanied by many cardiovascular complications. There is a need to identify the trigger mechanisms that lead to the production of in vivo activating factors. We review here mechanisms for cell activation in the microcirculation and specifically the production of humoral cell activators in physiological shock. The elevated levels of activating factors in plasma could be traced to the action of pancreatic enzymes in the ischemic intestine. New interventions against the production of the activators are proposed. The evidence suggests that pancreatic enzymes in the ischemic intestine may attack several tissue components and generate cellular activators that are associated with multiorgan dysfunction in physiological shock.
NON-DESTRUCTIVE ANALYSES FOR MODERN PAINTINGS: THE RUSSIAN AVANT-GARDE CASE

It is now common practice to analyze works of art using non-destructive, non-invasive techniques like classical radiography, macro-photography, infra-red reflectography (IRR) and ultraviolet (UV). This image analysis, unfortunately, does not sufficiently establish with a high level of accuracy the techniques and materials used in painting. Chemical analysis is used instead, for example, to identify the nature of the pigments. In the past, chemical analyses were conducted using destructive techniques such as cross-section or micro sample to SEM analyses. Relatively new non-destructive analyses like X-Ray Fluorescence and Raman Spectroscopy are currently used in order to analyze works of art and give chemical results. The results of these tests on works of art are very important for conservators, art-historians and keepers of private or public museum collections. These investigations reveal information which is of historical interest: the materials that were used and which can be compared with the ones that were available at a certain period in a particular region. During a study of many of the Russian Avant-guard paintings (1910-1930) a productive collaboration with art historians gave us the possibility to make important discoveries using our non destructive analysis. Three case studies are presented here. The first one shows how non destructive techniques help us to discover how the painter K. Malevitch (1879-1935) used pigments in different ways to obtain specific visual results corresponding to his aesthetic research. The second one shows how advanced image analysis helped us to discover a M. Larionov painting (1881-1964) that we were later able to associate with other known works. The last example concerns A. Exter's (1882-1947) series.
Reflection and Action Under Scarce Resources: Theoretical Principles and Empirical Study

We define and exercise the expected value of computation as a fundamental component of reflection about alternative inference strategies. We present a portion of Protos research focused on the interlacing of reflection and action under scarce resources, and discuss how the techniques have been applied in a high-stakes medical domain. The work centers on endowing a computational agent with the ability to harness incomplete characterizations of problem-solving performance to control the amount of effort applied to a problem or subproblem, before taking action in the world or turning to another problem. We explore the use of the techniques in controlling decision-theoretic inference itself, and pose the approach as a model of rationality under scarce resources.