Miracle-dz/UniFAR-FTUs huggingface dataset:
Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures.
Construction and Characterization of Recombinant HSV-1 Expressing Early Growth Response-1

Early Growth response-1 (Egr-1) is a transcription factor that possesses a variety of biological functions. It has been shown to regulate HSV-1 gene expression and replication in different cellular environments through the recruitment of distinct cofactor complexes. Previous studies demonstrated that Egr-1 can be induced by HSV-1 infection in corneal cells but the level was lower compared to other cell types. The primary goal of this report is to generate a recombinant HSV-1 constitutively expressing Egr-1 and to investigate the regulation of viral replication in different cell types or in animals with Egr-1 overexpression. The approach utilized was to introduce Egr-1 into the BAC system containing complete HSV-1 (F) genome. To assist in the insertion of Egr-1, a gene cassette was constructed that contains the Egr-1 gene flanked byloxP sites. In this clone Egr-1 is expressed under control of CMV immediate-early promoter followed by another gene cassette expressing the enhanced green fluorescent protein (EGFP) under the control of the elongation factor 1α (EF-1 α) promoter. The constructed recombinant viruses were completed containing the Egr-1 gene within the viral genome and the expression was characterized by qRT-PCR and Western blot analyses. Our results showed that Egr-1 transcript and protein can be generated and accumulated upon infection of recombinant virus in Vero and rabbit corneal cells SIRC. This unique virus therefore is useful for studying the effects of Egr-1 during HSV-1 replication and gene regulation in epithelial cells and neurons.
Functional complementation of UL3.5-negative pseudorabies virus by the bovine herpesvirus 1 UL3.5 homolog

The UL3.5 gene is positionally conserved but highly variable in size and sequence in different members of the Alphaherpesvirinae and is absent from herpes simplex virus genomes. We have shown previously that the pseudorabies virus (PrV) UL3.5 gene encodes a nonstructural protein which is required for secondary envelopment of intracytoplasmic virus particles in the trans-Golgi region. In the absence of UL3.5 protein, naked nucleocapsids accumulate in the cytoplasm, release of infectious virions is drastically reduced, and plaque formation in cell culture is inhibited (W. Fuchs, B. G. Klupp, H. Granzow, H.-J. Rziha, and T. C. Mettenleiter, J. Virol. 70:3517-3527, 1996). To assay functional complementation by a heterologous herpesviral UL3.5 protein, the UL3.5 gene of bovine herpesvirus 1 (BHV-1) was inserted at two different sites within the genome of UL3.5-negative PrV. In cells infected with the PrV recombinants the BHV-1 UL3.5 gene product was identified as a 17-kDa protein which was identical in size to the UL3.5 protein detected in BHV-1-infected cells. Expression of BHV-1 UL3.5 compensated for the lack of PrV UL3.5, resulting in a ca. 1,000-fold increase in virus titer and restoration of plaque formation in cell culture. Also, the intracellular block in viral egress was resolved by the BHV-1 UL3.5 gene. We conclude that the UL3.5 proteins of PrV and BHV-1 are functionally related and are involved in a common step in the egress of alphaherpesviruses.
Admission control in Flow-Aware Multi-Topology Adaptive Routing

Flow-Aware Multi-Topology Adaptive Routing (FAMTAR) is a new mechanism which provides the ability to use multiple paths between two points in a network. When the primary path becomes congested, a new path is found and used. However, when all possible paths are congested, new flows are still accepted on one of the congested paths which degrades the observed quality of service. Therefore, in this paper, two admission control mechanisms for FAMTAR are presented and analyzed. The main goal of the algorithms is to restrict new flows' access to congested paths and force them to wait for resources to become available. We propose two different methods to determine whether an available path for a new flow is congested or not. Moreover, we propose a mechanism which assures the transmission of selected flows (e.g. emergency calls) through paths with minimum total delay. The presented analysis shows the advantages of the introduced proposals and allows to estimate the potential gain from using these mechanisms.
Effective authorization for the Web of Things

The momentum gained by the Internet of Things (IoT) has lead technology to be sufficiently mature to finally reach the market. The expectations and concerns of users around new products are primarily related to the possibility to interact with things in a seamless and effective way and, above all, to do so securely. Within this context, the main pillars required to support a sustainable and practical IoT are: interoperability, discoverability, and authorization. Based on the concepts and experience gained with the traditional Internet, the Web of Things (WoT) paradigm is chartered to address the former two issues. However, fast-developed and simplistic vertical approaches, due to the rush to launch IoT products, have not considered authorization adequately. Access to smart objects typically occurs through product-bound Cloud platforms, which mediate between vendor-specific smartphone apps and objects. Notwithstanding, effective mechanisms to manage authorized access to resources are required to really make simple and safe to use and share things. In this paper, we propose a standard-based authorization framework for WoT applications, which allows to effectively enforce fine-grained access policies to authorized parties. An implementation is presented to highlight the simplicity of the proposed approach and the benefits that it can introduce.
Are continuity clinic patients less satisfied when the resident is postcall?

Due to recent public debate and newly imposed resident work hour restrictions, we decided to investigate the relationship of resident call status to their ambulatory patients’ satisfaction. Resident continuity clinic patients were asked to rate their level of satisfaction on a 10-point Likert-type scale. Using multiple regression approaches, these data were then assessed as a function of resident call status. We found that in 646 patient encounters, patient satisfaction scores were significantly less when the resident was postcall, 8.99±1.8, than when not postcall, 9.31±1.3. We herein discuss etiologies and implications of these findings for both patient care and medical education.
Modeling and Evaluation of LTE in Intelligent Transportation Systems

The term Intelligent Transportation Systems (ITS) refers to adding information and communications technology to transport infrastructure and ve- hicles. The IEEE 802.11p standard is considered the main candidate for com- munication within the context of ITS and it performs well for active safety use cases thanks to its very low delay. Nonetheless, there are still some problems that originate mostly from the decentralized ad-hoc nature of the protocol, that lead us to believe that the information exchange in ITS can also be handled via a different kind of network. In this paper, the technical feasibility of the use of LTE for ITS communication is examined. A model was built simulating the function of the LTE evolved Radio Access Network (eRAN) operating in a ve- hicular environment and its performance is evaluated. The results are encourag- ing and indicate that LTE can be used to handle certain types of traffic in a ve- hicular network.
The Hilbert Function, Algebraic Extractors, and Recursive Fourier Sampling

In this paper, we apply tools from algebraic geometry to prove new results concerning extractors for algebraic sets, the recursive Fourier sampling problem, and VC dimension. We present a new construction of an extractor which works for algebraic sets defined by polynomials over GF(2) of substantially higher degree than the current state-of-the-art construction. We also exactly determine the GF(2)-polynomial degree of the recursive Fourier sampling problem and use this to provide new partial results towards a circuit lower bound for this problem. Finally, we answer a question concerning VC dimension, interpolation degree and the Hilbert function.
Estonia – Highly Unequal but Classless?

In this short essay, we try to assess the utility of class analyses for understanding the contemporary Estonian society. Erik Wright (2009) identiﬁ es three strands of class analysis: a stratiﬁ cation approach, a Weberian approach and a Marxist approach. We address the following questions: Which kind of class analysis is most present in Estonia today? Which is most needed? The main conclusion is that due to this marginalisation of class discourse, as well as the power of national/ethnic discourse and transitional culture, those most economically vulnerable were deprived of the cultural and discursive resources to resist the most the extreme market-oriented policies. The conditions for structuration of class relations were created, while the class and inequality discourse was marginalised.
A Real-time Full-HD 2D-to-3D Conversion System Using Multicore Technology

The advancement of visual technology and the maturity of display process technique enable monitor industry to put forth multi-view stereo display systems, which allow consumers to watch 3D images with naked eyes. However, due to the insufficient 3D original videos, we are unable to achieve the end of enjoying 3D effect through stereo display. Therefore, this paper aims to provide a real-time algorithm for 2D-to-3D conversion, through which 2D video will be accompanied with a depth image so that one can obtain 3D images through auto stereoscopic display. The proposed algorithm focuses on the depth of background scenes and the active objects, while extracting depth information from the two for complete processing of depth generation. Since the production of depth information always requires heavy computation, we adapt VIA¡¦s embedded systems with a 1.6GHz CPU, as well as nVIDIA CUDA (compute unified device architecture) technology which contains 256 core processor with the clock rate of each processor up to 950MHz. When accompanied with our proposed CUDA parallelization technique, the experimental results show an 83% of recognition rate for depth image, and a display rate of 32.52 frames per second in Full-HD format (1920x1088 pixels).
RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae

RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning—possibly mediated by intrinsically disordered protein segments—is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication.
A simple HPLC method to determine urinary phenylmercapturic acid and its application to gasoline station attendants to biomonitor occupational exposure to benzene at less than 1 ppm

The objective of this study was to establish a hand-saving method to measure phenylmercapturic acid (PMA) and to examine urinary PMA as a marker of occupational exposure to benzene at levels less than 1 ppm. A simple HPLC method was developed to analyse PMA by monitoring absorption at 195 nm of the ef? uent from an ODS-3 column with acetonitrile–methanol–perchloric acid–water as a mobile phase. The detection limit of the method was 0.2 μg l−1 with sufficient reproducibility. The method was applied to end-of-shift urine samples from 70 gasoline station attendants exposed to up to 107 ppb benzene, and 20 non-exposed controls of both sexes. Time-weighted average (TWA) exposure to benzene was measured by diffusive sampling. A regression analysis was applied to examine the quantitative relationship between the intensity of exposure to benzene and PMA in the end-of-shift urine samples. Multiple regression analysis showed no effects of age, sex, smoking and co-exposure to toluene and xylenes on urinary PMA. There was a linear relationship between TWA benzene exposure and urinary PMA (r = 0.60–0.67, P < 0.01). Background PMA in urine of the non-exposed controls was low and scattering of PMA around the regression line was narrow so that those with 20 ppb benzene exposure can be separated from the non-exposed by urinalysis for PMA. Thus, urinary PMA is sensitive enough for biological exposure monitoring of those exposed to less than 1 ppm benzene.
The NSL Complex Regulates Housekeeping Genes in Drosophila

MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP–seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP–seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication–related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.
Pseudo-absences, pseudo-models and pseudo-niches: pitfalls of model selection based on the area under the curve

The area under the curve (AUC) of the receiver operator characteristic (ROC) graph is regarded as an objective measure of the discrimination accuracy of predictive models. AUC scores calculated from background values, or pseudo-absences, have been proposed as a method of model selection for species distribution models (SDMs) fitted to presence-only data. However, the utility of AUC as a measure of model performance when data on confirmed absence are unavailable has not been fully investigated. We fitted SDMs using informative climatic variables for 2000 species of Mesoamerican trees. As a reference, we also built ‘pseudo-models’ using Gaussian random fields with no biological meaning. AUC correctly selected SDMs fitted to single environmental variables over ‘pseudo-models’ fitted to single random fields in almost all cases. However, when all seven variables were included in the models, AUC erroneously selected complex pseudo-models over complex climate models in 17% of the cases. The spatial distribution patterns predicted by the pseudo-models differed from the results derived from climate-based models, even when overall AUC scores were similar. Both model and pseudo-model AUC values increased when presence points were few and spatially aggregated. The results show that AUC calculated from presence-only data can be an unreliable guide for model selection. Pseudo-absences have ill-defined properties that challenge the interpretation of AUC values. Inference on multidimensional niche spaces should not be supported by AUC values calculated using pseudo-absences.
Design of Constrained Causal Stable IIR Filters Using a New Second- Order-Cone-Programming-Based Model-Reduction Technique

This brief proposes a new method for designing infinite-impulse response (IIR) filter with peak error and prescribed flatness constraints. It is based on the model reduction of a finite-impulse response function that satisfies the specification by extending a method previously proposed by Brandenstein. The proposed model-reduction method retains the denominator of the conventional techniques and formulates the optimal design of the numerator as a second-order cone programming problem. Therefore, linear and convex quadratic inequalities such as peak error constraints and prescribed number of zeros at the stopband for IIR filters can be imposed and solved optimally. Moreover, a method is proposed to express the denominator of the model-reduced IIR filter as a polynomial in integer power of z, which efficiently facilitates its polyphase implementation in multirate applications. Design examples show that the proposed method gives better performance, and more flexibility in incorporating a wide variety of constraints than conventional methods
Interactions between colon cancer cells and hepatocytes in rats in relation to metastasis

Adhesion of cancer cells to endothelium is considered an essential step in metastasis. However, we have shown in a previous study that when rat colon cancer cells are administered to the vena portae, they get stuck mechanically in liver sinusoids. Then, endothelial cells retract rapidly and cancer cells bind to hepatocytes. We investigated the molecular nature of these interactions between colon cancer cells and hepatocytes. Cancer cells in coculture with hepatocytes became rapidly activated with distinct morphological changes. Cancer cells formed long cytoplasmic protrusions towards hepatocytes in their close vicinity and these protrusions attached to microvilli of hepatocytes. Then, adhering membrane areas were formed by both cell types. Integrin subunits αv, α6 and β1 but not αL, β2, β3 and CD44 and CD44v6 were expressed on the cancer cells. In conclusion, colon cancer cells show an active behaviour to bind to hepatocytes, likely involving the integrin subunits av, a6 and B1, indicating that early events in colon cancer metastasis in liver are distinctly different than assumed thus far.
The sparse matrix vector product on GPUs

The sparse matrix vector product (SpMV) is a paramount operation in engineering and scientific computing and, hence, has been a subject of intense research for long. The irregular computations involved in SpMV make its optimization challenging. Therefore, enormous effort has been devoted to devise data formats to store the sparse matrix with the ultimate aim of maximizing the performance. The Graphics Processing Units (GPUs) have recently emerged as platforms that yield outstanding acceleration factors. Currently, SpMV implementations for NVIDIA-GPUs have already appeared on the scene. This work proposes and evaluates a new implementation of SpMV for GPUs based on a new matrix storage format, called ELLPACK-R, and compares it against a variety of formats proposed elsewhere. The most important qualities of this new format is that (1) no preprocessing of the sparse matrix is required, and (2) the resulting SpMV algorithm is very regular. The comparative evaluation of this new SpMV approach has been carried out based on a representative set of test matrices. The results show that the SpMV approach based on ELLPACK-R turns out to be superior to the previous strategies used so far. Moreover, a comparison with standard state-of-the-art superscalar processors reveals that significant speedup factors are achieved
A review of the development and application of the Web impact factor

Since 1996, hyperlinks have been studied extensively by applying existing bibliometric methods. The Web impact factor (WIF), for example, is the online counterpart of the journal impact factor. This paper reviews how this link‐based metric has been developed, enhanced and applied. Not only has the metric itself undergone improvement but also the relevant data collection techniques have been enhanced. WIFs have also been validated by significant correlations with traditional research measures. Bibliometric techniques have been further applied to the Web and patterns that might have otherwise been ignored have been found from hyperlinks. This paper concludes with some suggestions for future research.