Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of Strand Replacement Synthesis for Plasmid DNA Transferred by Conjugation

ABSTRACT A single strand of plasmid DNA is transferred during conjugation. We examined the mechanism of complementary strand synthesis in recipient cells following conjugative mobilization of derivatives of the IncQ plasmid R1162. A system for electroporation of donor cells, followed by immediate mating, was used to eliminate plasmid-specific replicative functions. Under these conditions, Escherichia coli recipients provided a robust mechanism for initiation of complementary strand synthesis on transferred DNA. In contrast, plasmid functions were important for efficient strand replacement in recipient cells of Salmonella enterica serovar Typhimurium. The mobilizing vector for R1162 transfer, the IncP1 plasmid R751, encodes a DNA primase with low specificity for initiation. This protein increased the frequency of transfer of R751 into Salmonella, but despite its low specificity, it was inactive on the R1162 derivatives. The R751 primase was slightly inhibitory for the transfer of both R751 and R1162 into E. coli. The results show that there is a chromosomally encoded mechanism for complementary strand synthesis of incoming transferred DNA in E. coli, while plasmid-specific mechanisms for this synthesis are important in Salmonella.
Distance-adaptive online RSA algorithms for heterogeneous flex-grid networks

Flex-grid elastic optical networks are an enabling technology for future heterogeneous on-demand optical bandwidth services. Heterogeneous means that optical connection requests for different services requiring different data rates would coexist in the network. In this context, Routing and Spectrum Assignment (RSA) algorithms face the challenge of making a fair allocation of resources, providing a similar blocking performance to all the services. In this paper, we review existing RSA proposals applicable to heterogeneous flex-grid networks, evaluating (i) their blocking performance averaged among services, and (ii) the fairness in the blocking observed by each individual service. In addition, we propose the Partial-Sharing-Partitioning (PSP), a scheme to balance both aforementioned metrics. We concentrate on a distance-adaptive scenario, where the same connection request can be carried with different modulations, associated to different spectral efficiencies and optical reaches. Our simulation results in the Net2Plan tool explore the interplay between average blocking and fairness. We observe that many classical RSA algorithms produce unfair allocations, while PSP permits tuning the balance between both metrics. The algorithms developed are publicly available in the open-source Net2Plan repository.
Path tracking control of tracked vehicles

A path tracking control algorithm for tracked surface drilling machines is presented. The general dynamic model of such vehicle is simulated including track-soil interactions. The controller is based on feedback linearization of the equations with feedforward friction compensation. It linearizes the complex force-slip relationship to relate the states of the system to the inputs. The controller based on simplified models is applied to the detailed simulated model of the vehicle. The result is an accurate control of the lateral offset and forward velocity error along a path.
Identification of OpuC as a Chill-Activated and Osmotically Activated Carnitine Transporter in Listeria monocytogenes

ABSTRACT The food-borne pathogen Listeria monocytogenes is notable for its ability to grow under osmotic stress and at low temperatures. It is known to accumulate the compatible solutes glycine betaine and carnitine from the medium in response to osmotic or chill stress, and this accumulation confers tolerance to these stresses. Two permeases that transport glycine betaine have been identified, both of which are activated by hyperosmotic stress and one of which is activated by low temperature. An osmotically activated transporter for carnitine, OpuC, has also been identified. We have isolated a Tn917-LTV3 insertional mutant that could not be rescued from hyperosmotic stress by exogenous carnitine. The mutant, LTS4a, grew indistinguishably from a control strain (DP-L1044) in the absence of stress or in the absence of carnitine, but DP-L1044 grew substantially faster under osmotic or chill stress in the presence of carnitine. LTS4a was found to be strongly impaired in KCl-activated as well as chill-activated carnitine transport. 13C nuclear magnetic resonance spectroscopy of perchloric acid extracts showed that accumulation of carnitine by LTS4a was negligible under all conditions tested. Direct sequencing of LTS4a genomic DNA with a primer based on Tn917-LTV3 yielded a 487-bp sequence, which allowed us to determine that the opuC operon had been interrupted by the transposon. It can be concluded that opuC encodes a carnitine transporter that can be activated by either hyperosmotic stress or chill and that the transport system plays a significant role in the tolerance of L. monocytogenes to both forms of environmental stress.
Identification of Differential Gene Expression Patterns after Acute Exposure to High and Low Doses of Low-LET Ionizing Radiation in a Reconstituted Human Skin Tissue

In this study we utilized a systems biology approach to identify dose- (0.1, 2.0 and 10 Gy) and time- (3 and 8 h) dependent responses to acute ionizing radiation exposure in a complex tissue, reconstituted human skin. The low dose used here (0.1 Gy) falls within the range of certain medical diagnostic procedures. Of the two higher doses used, 2.0 Gy is typically administered for radiotherapy, while 10 Gy is lethal. Because exposure to any of these doses is possible after an intentional or accidental radiation events, biomarkers are needed to rapidly and accurately triage potentially exposed individuals. Here, tissue samples were acutely exposed to X-ray-generated low-linear-energy transfer (LET) ionizing radiation, and direct RNA sequencing (RNA-seq) was used to quantify altered transcripts. The time points used for this study aid in assessing early responses to exposure, when key signaling pathways and biomarkers can be identified, which precede and regulate later phenotypic alterations that occur at high doses, including cell death. We determined that a total of 1,701 genes expressed were significantly affected by high-dose radiation, with the majority of genes affected at 10 Gy. Expression levels of a group of 29 genes, including GDF15, BBC3, PPM1D, FDXR, GADD45A, MDM2, CDKN1A, TP53INP1, CYCSP27, SESN1, SESN2, PCNA and AEN, were similarly altered at both 2 and 10 Gy, but not 0.1 Gy, at both time points. A much larger group of upregulated genes, including those involved in inflammatory responses, was significantly altered only after 10 Gy irradiation. At high doses, downregulated genes were associated with cell cycle regulation and exhibited an apparent linear response between 2 and 10 Gy. While only a few genes were significantly affected by 0.1 Gy irradiation, using stringent statistical filters, groups of related genes regulating cell cycle progression and inflammatory responses consistently exhibited opposite trends in their regulation compared to high-dose irradiated groups. Differential regulation of PLK1 signaling at low- and high-dose irradiation was confirmed using qRT-PCR. These results indicate that some alterations in gene expression are qualitatively different at low and high doses of ionizing radiation in this model system. They also highlight potential biomarkers for radiation exposure that may precede the development of overt physiological symptoms in exposed individuals.
Impact of the accuracy of automatic segmentation of cell nuclei clusters on classification of thyroid follicular lesions

Automatic segmentation of cell nuclei clusters is a key building block in systems for quantitative analysis of microscopy cell images. For that reason, it has received a great attention over the last decade, and diverse automatic approaches to segment clustered nuclei with varying levels of performance under different test conditions have been proposed in literature. To the best of our knowledge, however, so far there is no comparative study on the methods. This study is a first attempt to fill this research gap. More precisely, the purpose of this study is to present an objective performance comparison of existing state‐of‐the‐art segmentation methods. Particularly, the impact of their accuracy on classification of thyroid follicular lesions is also investigated “quantitatively” under the same experimental condition, to evaluate the applicability of the methods. Thirteen different segmentation approaches are compared in terms of not only errors in nuclei segmentation and delineation, but also their impact on the performance of system to classify thyroid follicular lesions using different metrics (e.g., diagnostic accuracy, sensitivity, specificity, etc.). Extensive experiments have been conducted on a total of 204 digitized thyroid biopsy specimens. Our study demonstrates that significant diagnostic errors can be avoided using more advanced segmentation approaches. We believe that this comprehensive comparative study serves as a reference point and guide for developers and practitioners in choosing an appropriate automatic segmentation technique adopted for building automated systems for specifically classifying follicular thyroid lesions. © 2014 International Society for Advancement of Cytometry
Supporting Knowledge Work by Observing Paper-Based Activities on the Physical Desktop

Despite the progress in personal information management, the desks of knowledge workers have remained untouched, justified by the claim that the paperless office is imminent. This led to a huge gap between the electronic world and the physical world. This paper combines the Semantic Desktop, methods of desk organization, and user observation together in order to bridge this gap. It focuses on paper artifacts and makes use of how knowledge workers organize them and interact with them. Paper artifacts are automatically observed, identified, and integrated into a model of the physical world. Moreover, paper documents are introduced into the personal knowledge space. A history of present and past desk layouts enables knowledge workers to search for information that was once present on their desks.
Ieee Transactions on Image Processing 1 Critically Sampled Wavelets with Composite Dilations

—Wavelets with composite dilations provide a general framework for the construction of waveforms defined not only at various scales and locations, as traditional wavelets, but also at various orientations and with different scaling factors in each coordinate. As a result, they are useful to analyze the geometric information which often dominate multidimensional data much more efficiently than traditional wavelets. The shearlet system, for example, is a particular well-known realization of this framework which provides optimally sparse representations of images with edges. In this work, we further investigate the constructions derived from this approach to develop critically sampled wavelets with composite dilations for the purpose of image coding. Not only we show that the many nonredundant directional constructions recently introduced in the literature can be derived within this setting. We also introduce new critically sampled discrete transforms which achieve much better non-linear approximation rates than traditional discrete wavelet transforms, and outperform the other critically sampled multiscale transforms recently proposed.
Calmodulin Is an Auxiliary Subunit of KCNQ2/3 Potassium Channels

Calmodulin (CaM) was identified as a KCNQ2 and KCNQ3 potassium channel-binding protein, using a yeast two-hybrid screen. CaM is tethered constitutively to the channel, in the absence or presence of Ca2+, in transfected cells and also coimmunoprecipitates with KCNQ2/3 from mouse brain. The structural elements critical for CaM binding to KCNQ2 lie in two conserved motifs in the proximal half of the channel C-terminal domain. Truncations and point mutations in these two motifs disrupt the interaction. The first CaM-binding motif has a sequence that conforms partially to the consensus IQ motif, but both wild-type CaM and a Ca2+-insensitive CaM mutant bind to KCNQ2. The voltage-dependent activation of the KCNQ2/3 channel also shows no Ca2+ sensitivity, nor is it affected by overexpression of the Ca2+-insensitive CaM mutant. On the other hand, KCNQ2 mutants deficient in CaM binding are unable to generate detectable currents when coexpressed with KCNQ3 in CHO cells, although they are expressed and targeted to the cell membrane and retain the ability to assemble with KCNQ3. A fusion protein containing both of the KCNQ2 CaM-binding motifs competes with the full-length KCNQ2 channel for CaM binding and decreases KCNQ2/3 current density in CHO cells. The correlation of CaM binding with channel function suggests that CaM is an auxiliary subunit of the KCNQ2/3 channel.
So Close and Yet So Far: Information Technology and the Spatial Distribution of Customer Service

Where should firms locate? As communication technologies spread across city, region,and country boundaries, and communication channels multiply, many firms can potentially relocate some of their activities to regions with lower costs. While manufacturing has long been globalizing, IT is enabling a new wave focused on services. Spatial relocation is attractive to companies faced with the incessant pressure to control costs and information technologies can help firms transcend location boundaries. But these same technologies may also confer renewed importance to local assets that are hard to replicate in remote locations. This paper develops a framework to analyze these effects by estimating the regional demand for customer service representatives of a homogenous set of Fortune 1000 manufacturing firms. The model is estimated using firm-level data and the estimated demand structure is used to assess the effects of technology on customer volume, location choices and cost savings. A 10 percent increase in the use of Internet applications is found to lead to a 2.5 percent decrease in the firm’s employment of agents nationally. Moreover, the same increase reduces the willingness of firms to pay for regional benefits (technology “levels” the field between regions). However, the cost savings from the associated relocation are surprisingly small, averaging 1.3 percent of unit costs. Finally, the research shows that regional preferences vary widely among firms, suggesting that sensitivity to cost is highly firm-specific and that the importance of local assets does not vanish. Overall, these results show a positive relationship between technology and firms’ price sensitivity, but not on the scale of a massive spatial reorganization. Firm-specific regional preferences still matter.
DYNAMIC MECHANICAL PROPERTIES OF TOUGHENED POLYAMIDE COMPOSITES

ABSTRACT The effect of incorporating thermoplastic rubber on the dynamic mechanical properties, storage and loss moduli, of virgin and recycled glass-fiber-reinforced polyamide 66 has been investigated in this study. Styrene-Ethylene–Butylene-Styrene and Ethylene–Propylene grafted with maleic anhydride were used as elastomers for toughening. Dynamic mechanical properties of the composites were examined by the rotational rheometry. Shear storage and loss moduli of recycled and virgin materials were measured against frequency. Also the variation of storage modulus of the virgin composites was measured against temperature by conducting a series of torsion tests. Both dynamic storage and loss moduli of the composites were found to increase with increasing glass fiber and rubber contents. Recycled composites had lower values of dynamic modulus compared to that of virgin composites; however by proper combining of fiber and rubber into the recycled material, its modulus fairly matches that of the virgin material. Addition of rubber to virgin composites causes a reduction in
Feature Extraction With Deep Neural Networks by a Generalized Discriminant Analysis

We present an approach to feature extraction that is a generalization of the classical linear discriminant analysis (LDA) on the basis of deep neural networks (DNNs). As for LDA, discriminative features generated from independent Gaussian class conditionals are assumed. This modeling has the advantages that the intrinsic dimensionality of the feature space is bounded by the number of classes and that the optimal discriminant function is linear. Unfortunately, linear transformations are insufficient to extract optimal discriminative features from arbitrarily distributed raw measurements. The generalized discriminant analysis (GerDA) proposed in this paper uses nonlinear transformations that are learnt by DNNs in a semisupervised fashion. We show that the feature extraction based on our approach displays excellent performance on real-world recognition and detection tasks, such as handwritten digit recognition and face detection. In a series of experiments, we evaluate GerDA features with respect to dimensionality reduction, visualization, classification, and detection. Moreover, we show that GerDA DNNs can preprocess truly high-dimensional input data to low-dimensional representations that facilitate accurate predictions even if simple linear predictors or measures of similarity are used.
DeTrust: Defeating Hardware Trust Verification with Stealthy Implicitly-Triggered Hardware Trojans

Hardware Trojans (HTs) inserted at design time by malicious insiders on the design team or third-party intellectual property (IP) providers pose a serious threat to the security of computing systems. Researchers have proposed several hardware trust verification techniques to mitigate such threats, and some of them are shown to be able to effectively flag all suspicious HTs implemented in the Trust-Hub hardware backdoor benchmark suite. No doubt to say, adversaries would adjust their tactics of attacks accordingly and it is hence essential to examine whether new types of HTs can be designed to defeat these hardware trust verification techniques. In this paper, we present a systematic HT design methodology to achieve the above objective, namely \emph{DeTrust}. Given an HT design, DeTrust keeps its original malicious behavior while making the HT resistant to state-of-the-art hardware trust verification techniques by manipulating its trigger designs. To be specific, DeTrust implements stealthy implicit triggers for HTs by carefully spreading the trigger logic into multiple sequential levels and combinational logic blocks and combining the trigger logic with the normal logic, so that they are not easily differentiable from normal logic. As shown in our experimental results, adversaries can easily employ DeTrust to evade hardware trust verification. We close with a discussion on how to extend existing solutions to alleviate the threat posed by DeTrust. However, they generally suffer from high computational complexity, calling for more advanced techniques to ensure hardware trust.
Interrupted time series regression for the evaluation of public health interventions: a tutorial

Abstract Interrupted time series (ITS) analysis is a valuable study design for evaluating the effectiveness of population-level health interventions that have been implemented at a clearly defined point in time. It is increasingly being used to evaluate the effectiveness of interventions ranging from clinical therapy to national public health legislation. Whereas the design shares many properties of regression-based approaches in other epidemiological studies, there are a range of unique features of time series data that require additional methodological considerations. In this tutorial we use a worked example to demonstrate a robust approach to ITS analysis using segmented regression. We begin by describing the design and considering when ITS is an appropriate design choice. We then discuss the essential, yet often omitted, step of proposing the impact model a priori. Subsequently, we demonstrate the approach to statistical analysis including the main segmented regression model. Finally we describe the main methodological issues associated with ITS analysis: over-dispersion of time series data, autocorrelation, adjusting for seasonal trends and controlling for time-varying confounders, and we also outline some of the more complex design adaptations that can be used to strengthen the basic ITS design.
Bigrams in registers, domains, and varieties: a bigram gravity approach to the homogeneity of corpora

In this paper, I explore how a new measure of collocational attraction proposed by Daudaravičius, & Marcinkevičienė (2004), lexical gravity G , can distinguish different registers and, hence, degrees of within-corpus homogeneity. To that end, I compute G -values for all bigrams in the BNC Baby and perform three different tests. First, I explore to what degree their averages reflect what is known about spoken vs. written data. Second, I use hierarchical agglomerative cluster analysis to determine how well a cluster analysis of the G -values can re-create the register structure of the BNC Baby (where I am using a classification of the BNC Baby into four registers and 19 sub-registers as a gold-standard). Finally, I compare the performance of the G -values in the cluster analysis to that of a more established measure of collocational strength, the t -score. The results show that the measure of lexical gravity not only distinguishes speaking and writing very reliably, but also reflects the well-known use of more frequent high-attraction bigrams in speech. Moreover, the gravity-based cluster analysis of the 19 sub-registers of the BNC Baby recognizes the corpus’ register structure perfectly and, thus, outperforms the better-known t -score.
Par3 functions in the biogenesis of the primary cilium in polarized epithelial cells

Par3 is a PDZ protein important for the formation of junctional complexes in epithelial cells. We have identified an additional role for Par3 in membrane biogenesis. Although Par3 was not required for maintaining polarized apical or basolateral membrane domains, at the apical surface, Par3 was absolutely essential for the growth and elongation of the primary cilium. The activity reflected its ability to interact with kinesin-2, the microtubule motor responsible for anterograde transport of intraflagellar transport particles to the tip of the growing cilium. The Par3 binding partners Par6 and atypical protein kinase C interacted with the ciliary membrane component Crumbs3 and we show that the PDZ binding motif of Crumbs3 was necessary for its targeting to the ciliary membrane. Thus, the Par complex likely serves as an adaptor that couples the vectorial movement of at least a subset of membrane proteins to microtubule-dependent transport during ciliogenesis.
Highway map matching algorithm based on floating car data

Real-time traffic information is important in terms of easing highway congestion, while map matching is the basis for calculating real-time traffic information. This paper starts with the three factors of currently used algorithms in floating car map matching, namely distance, speed-direction, and connectivity. From there, the paper gives analysis on the characteristics of highway network and the efficiency problems of currently used algorithms, and proposes a new map matching model based on the gradual-removal of candidate roads. Based on this model, the paper gives the corresponding algorithm process and testing results of processing actual GPS data. It has been validated that this algorithm is of fine accuracy and is capable of meeting the efficiency requirements of map matching in large-scale floating car data on highway, therefore providing a feasible approach for highway map matching at present.