Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarchitectural Support for Program Code Integrity Monitoring in Application-specific Instruction Set Processors

Program code in a computer system can be altered either by malicious security attacks or by various faults in microprocessors. At the instruction level, all code modifications are manifested as bit flips. In this work, we present a generalized methodology for monitoring code integrity at run-time in application-specific instruction set processors (ASIPs), where both the instruction set architecture (ISA) and the underlying micro architecture can be customized for a particular application domain. We embed monitoring microoperations in machine instructions, thus the processor is augmented with a hardware monitor automatically. The monitor observes the processor's execution trace of basic blocks at run-time, checks whether the execution trace aligns with the expected program behavior, and signals any mismatches. Since microoperations are at a lower software architecture level than processor instructions, the microarchitectural support for program code integrity monitoring is transparent to upper software levels and no recompilation or modification is needed for the program. Experimental results show that our microarchitectural support can detect program code integrity compromises with small area overhead and little performance degradation
Roles of Angiotensin II Type 2 Receptor Stimulation Associated With Selective Angiotensin II Type 1 Receptor Blockade With Valsartan in the Improvement of Inflammation-Induced Vascular Injury

Background—To investigate the effect of angiotensin (Ang) II type 1 receptor (AT1) blocker on vascular remodeling and explore the possibility of the involvement of Ang II type 2 receptor (AT2) stimulation in this process, we examined the effects of the selective AT1 blocker valsartan on the vascular injury in wild-type (Agtr2+) and AT2-null (Agtr2−) mice. Methods and Results—Neointima formation and the proliferation of vascular smooth muscle cells (VSMCs) induced by cuff placement on the femoral artery were greater in Agtr2− mice than those in Agtr2+ mice. Treatment of mice with valsartan at a dose of 1 mg · kg−1 · d−1, which did not influence systolic blood pressure, significantly decreased neointima formation and the proliferation of VSMCs, whereas the valsartan was less effective in Agtr2− mice. Moreover, cuff placement increased the expression of monocyte chemoattractant protein-1 (MCP-1); inflammatory cytokines such as tumor necrosis factor (TNF)-&agr;, interleukin (IL)-6, and IL-1&bgr;; and infiltration of CD45-positive leukocytes and macrophages in the injured arteries and further enhanced them in Agtr2− mice, suggesting the antagonistic effects of AT1 and AT2 for vascular inflammation. Valsartan attenuated the expression of MCP-1, TNF-&agr;, IL-6, IL-1&bgr;, and infiltration of leukocytes and macrophages in the injured arteries; however, these effects of valsartan were less prominent in Agtr2− mice. Conclusions—These results suggest that the stimulation of the AT2 receptor after AT1 blockade is important in the improvement of the inflammatory vascular injury.
Interruption of the Ionic Lock in the Bradykinin B2 Receptor Results in Constitutive Internalization and Turns Several Antagonists into Strong Agonists

The DRY motif with the highly conserved R3.50 is a hallmark of family A G protein-coupled receptors (GPCRs). The crystal structure of rhodopsin revealed a salt bridge between R1353.50 and another conserved residue, E2476.30, in helix 6. This ionic lock was shown to maintain rhodopsin in its inactive state. Thus far, little information is available on how interruption of this ionic bond affects signaling properties of nonrhodopsin GPCRs, because the focus has been on mutations of R3.50, although this residue is indispensable for G protein activation. To investigate the importance of an ionic lock for overall receptor activity in a nonrhodopsin GPCR, we mutated R1283.50 and E2386.30 in the bradykinin (BK) B2 receptor (B2R) and stably expressed the constructs in HEK293 cells. As expected, mutation of R3.50 resulted in lack of G protein activation. In addition, this mutation led to considerable constitutive receptor internalization. Mutation of E6.30 (mutants E6.30A and E6.30R) also caused strong constitutive internalization. Most intriguingly, however, although the two E6.30 mutants displayed no increased basal phosphatidylinositol hydrolysis, they gave a response to three different B2R antagonists that was almost comparable to that obtained with BK. In contrast, swapping of R3.50 and E6.30, thus allowing the formation of an inverse ionic bond, resulted in rescue of the wild type phenotype. These findings demonstrate for the first time, to our knowledge, that interruption of the ionic lock in a family A GPCR can have distinctly different effects on receptor internalization and G protein stimulation, shedding new light on its role in the activation process.
Genotypic and phenotypic alterations in Epstein–Barr virus‐associated lymphoma

Epstein–Barr virus (EBV) is associated with numerous reactive and neoplastic lymphoproliferative disorders. In vitro, EBV infection can transform B‐lymphocytes and induce phenotypic alterations. This study presents the clinicopathological features of four cases with malignant lymphoma, which showed phenotypic and/or genotypic alterations during the course of the disease.
A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs.

Phylogenetic and chemical probing data indicate that a modular RNA motif, common to loop E of eucaryotic 5 S ribosomal RNA (rRNA) and the alpha-sarcin/ricin loop of 23 S rRNA, organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. The motif occurs in the 3' domain of 16 S rRNA at positions 1345-1350/1372-1376 (Escherichia coli numbering), within the three-way junction loop, which binds ribosomal protein S7, and which contains nucleotides that help to form the binding site for P-site tRNA in the ribosome. The motif also helps to structure a three-way junction within domain I of 23 S, which contains many universally conserved bases and which lies close in the primary and secondary structure to the binding site of r-protein L24. Several other highly conserved hairpin, internal, and multi-helix loops in 16 S and 23 S rRNA contain the motif, including the core junction loop of 23 S and helix 27 in the core of 16 S rRNA. Sequence conservation and range of variation in bacteria, archaea, and eucaryotes as well as chemical probing and cross-linking data, provide support for the recurrent and autonomous existence of the motif in ribosomal RNAs. Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in helix P10 of bacterial RNase P, in domain P7 of one sub-group of group I introns, and in domain 3 of one subgroup of group II introns.
LIPN-IIMAS at SemEval-2017 Task 1: Subword Embeddings, Attention Recurrent Neural Networks and Cross Word Alignment for Semantic Textual Similarity

In this paper we report our attempt to use, on the one hand, state-of-the-art neural approaches that are proposed to measure Semantic Textual Similarity (STS). On the other hand, we propose an unsupervised cross-word alignment approach, which is linguistically motivated. The neural approaches proposed herein are divided into two main stages. The first stage deals with constructing neural word embeddings, the components of sentence embeddings. The second stage deals with constructing a semantic similarity function relating pairs of sentence embeddings. Unfortunately our competition results were poor in all tracks, therefore we concentrated our research to improve them for Track 5 (EN-EN).
Global view of enhancer–promoter interactome in human cells

Significance In eukaryotes, gene expression is controlled by short regulatory DNA sequences called enhancers. Understanding how an enhancer selects its target promoter(s) is a major challenge in the field of gene regulation. Advances in genomic technologies have enabled rapid and comprehensive identification of active promoters and enhancers for many cell types. However, there is a lack of methods to link bona fide enhancers and their target promoters. Here, we develop and integrate multiple genomic features into a statistical predictor for enhancer–promoter interactions. Systematic analyses of the predicted interactions across 12 cell types reveals several global features of enhancer–promoter communication. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying enhancer and promoter communication. Enhancer mapping has been greatly facilitated by various genomic marks associated with it. However, little is available in our toolbox to link enhancers with their target promoters, hampering mechanistic understanding of enhancer–promoter (EP) interaction. We develop and characterize multiple genomic features for distinguishing true EP pairs from noninteracting pairs. We integrate these features into a probabilistic predictor for EP interactions. Multiple validation experiments demonstrate a significant improvement over state-of-the-art approaches. Systematic analyses of EP interactions across 12 cell types reveal several global features of EP interactions: (i) a larger fraction of EP interactions are cell type specific than enhancers; (ii) promoters controlled by multiple enhancers have higher tissue specificity, but the regulating enhancers are less conserved; (iii) cohesin plays a role in mediating tissue-specific EP interactions via chromatin looping in a CTCF-independent manner. Our approach presents a systematic and effective strategy to decipher the mechanisms underlying EP communication.
Fast unfolding of communities in large networks

We propose a simple method to extract the community structure of large networks. Our method is a heuristic method that is based on modularity optimization. It is shown to outperform all other known community detection methods in terms of computation time. Moreover, the quality of the communities detected is very good, as measured by the so-called modularity. This is shown first by identifying language communities in a Belgian mobile phone network of 2 million customers and by analysing a web graph of 118 million nodes and more than one billion links. The accuracy of our algorithm is also verified on ad hoc modular networks.
Ultra Scale-Down Characterization of the Impact of Conditioning Methods for Harvested Cell Broths on Clarification by Continuous Centrifugation—Recovery of Domain Antibodies from rec E. coli

The processing of harvested E. coli cell broths is examined where the expressed protein product has been released into the extracellular space. Pre‐treatment methods such as freeze–thaw, flocculation, and homogenization are studied. The resultant suspensions are characterized in terms of the particle size distribution, sensitivity to shear stress, rheology and solids volume fraction, and, using ultra scale‐down methods, the predicted ability to clarify the material using industrial scale continuous flow centrifugation. A key finding was the potential of flocculation methods both to aid the recovery of the particles and to cause the selective precipitation of soluble contaminants. While the flocculated material is severely affected by process shear stress, the impact on the very fine end of the size distribution is relatively minor and hence the predicted performance was only diminished to a small extent, for example, from 99.9% to 99.7% clarification compared with 95% for autolysate and 65% for homogenate at equivalent centrifugation conditions. The lumped properties as represented by ultra scale‐down centrifugation results were correlated with the basic properties affecting sedimentation including particle size distribution, suspension viscosity, and solids volume fraction. Grade efficiency relationships were used to allow for the particle and flow dynamics affecting capture in the centrifuge. The size distribution below a critical diameter dependant on the broth pre‐treatment type was shown to be the main determining factor affecting the clarification achieved. Biotechnol. Bioeng. 2014;111: 913–924. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
Role of Interference Alignment in Wireless Cellular Network Optimization

The emergence of interference alignment (IA) as a degrees-of-freedom optimal strategy motivates the need to investigate whether IA can be leveraged to aid conventional network utility maximization algorithms, which are typically only capable of finding locally optimal solutions. To test the usefulness of IA in this context, this paper proposes a two-stage optimization framework for the downlink of a G -cell multi-antenna network with K users/cell. The first stage of the proposed framework focuses on nulling interference from a set of dominant interferers using IA, while the second stage optimizes transmit and receive beamformers to maximize a network-wide utility using the IA solution as the initial condition. Further, this paper establishes a set of new feasibility results for partial IA that can be used to guide the number of dominant interferers to be nulled in the first stage. Through simulations on specific topologies of a cluster of base stations, it is observed that the impact of IA depends on the choice of the utility function and the presence of out-of-cluster interference. In the absence of out-of-cluster interference, the proposed framework outperforms straightforward optimization when maximizing the minimum rate, while providing marginal gains when maximizing sum rate. However, the benefit of IA is greatly diminished in the presence of significant out-of-cluster interference.
Persistent hyperCKemia: fourteen patients studied in retrospect

ABSTRACT— Fourteen patients with persistently raised serum creatine kinase activity (hyperCKemia) were studied in retrospect. Clinical and laboratory findings did not point to any established neuromuscular disorder. In 8, manual occupation with local muscle strain apparently caused the hyperCKemia despite a low total work load. One patient had subclinical hypothyroidism with a normal serum thyroxine and an elevated thyroid‐stimulating hormone level. CK normalized with L‐thyroxine therapy. In 2, including one manual worker, myoadenylate deaminase was deficient. The hyperCKemia remained unexplained in 4 patients.
Molecular cloning of a new member of TEKTIN family, Tektin4, located to the flagella of rat spermatozoa

Tektins are composed of a family of filament‐forming proteins associated with ciliary and flagellar microtubules. A new member of the TEKTIN gene family, which was designated as rat Tektin4, was obtained by PCR technique combined with yeast two‐hybrid screening. Rat Tektin4 cDNA consists of 1,341 bp encoding a 52 kDa protein of 447 amino acids. Tektin4 protein contains a Tektin domain including a nonapeptide signature sequence (RPNVELCRD), which is a prominent feature of Tektins. Its amino acid sequence showed 29% ∼ 58% identities to that of other Tektin family proteins registered in the public databases. Tektin4 gene, which was mapped to rat chromosome 10q12, is composed of six exons and spanning 5 kb. Reverse‐transcriptional‐PCR (RT‐PCR) analysis indicated that Tektin4 was predominantly expressed in testis and its expression was upregulated during testis development. In situ hybridization analysis showed that Tektin4 mRNA was localized in round spermatids in the seminiferous tubules of the rat testis. Tektin4 protein was predominantly localized in the flagella of spermatozoa, suggesting that it might works as a flagellar component requisite for flagellar stability or sperm motility. © 2005 Wiley‐Liss, Inc.
Fast-At: Fast Automatic Thumbnail Generation Using Deep Neural Networks

Fast-AT is an automatic thumbnail generation system based on deep neural networks. It is a fully-convolutional deep neural network, which learns specific filters for thumbnails of different sizes and aspect ratios. During inference, the appropriate filter is selected depending on the dimensions of the target thumbnail. Unlike most previous work, Fast-AT does not utilize saliency but addresses the problem directly. In addition, it eliminates the need to conduct region search over the saliency map. The model generalizes to thumbnails of different sizes including those with extreme aspect ratios and can generate thumbnails in real time. A data set of more than 70,000 thumbnail annotations was collected to train Fast-AT. We show competitive results in comparison to existing techniques.
THIS IS MY PARTNER, AND THIS IS MY … PARTNER'S PARTNER: CONSTRUCTING A POLYAMOROUS IDENTITY IN A MONOGAMOUS WORLD

According to the writings of members of the polyamorous community, polyamory is a type of nonmonogamous relationship orientation in which it is considered acceptable to love more than one person and emphasis is placed on openness and honesty within one's relationships. The proliferation of websites, E-mail groups and books on the topic since the mid 1990s mean that polyamory can be seen as a burgeoning sexual story (Plummer, 1995). However, very little has been written academically on the topic, despite its fascinating potential to challenge mainstream discourses of monogamy and infidelity and to reveal the constructed nature of “compulsory heterosexuality” (Rich, 1980). In this article I draw on social constructionist and personal construct psychology perspectives to examine the ways in which polyamorous individuals construct their personal and group identities in relation to conventional monogamy and to explore the implications of polyamory for a person's own sense of self.
Measuring and Improving the Quality of World Knowledge extracted from WordNet

WordNet is a lexical database that, among other things, arranges English nouns into a hierarchy ranked by specificity, providing links between a more general word and words that are specializations of it. For example, the word "mammal" is linked (transitively via some intervening words) to "dog" and to "cat. " This hierarchy bears some resemblance to the hierarchies of types (or properties, or predicates) often used in artificial intelligence systems. However, WordNet was not designed for such uses, and is organized in a way that makes it far from ideal for them. This report describes our attempts to arrive at a quantitative measure of the quality of the information that can be extracted from WordNet by interpreting it as a formal taxonomy, and to design automatic techniques for improving the quality by filtering out dubious assertions.
Analysing the Role of Environmental Stresses on Species Richness and the Process of Hierarchical Structuring of Species Abundances in Marine Gastropods communities at Suva (Fiji Islands)

Anthropogenic environmental stresses, especially physio-chemical pollution, are causing steadily increasing threat to many ecosystems, among which coastal marine communities in tropical shallow waters are especially sensitive. In particular, species-rich marine gastropod assemblages are doomed to bear sharp drops in species diversity when exposed to pollutants released offshore. Yet, the details of the process of decline in species diversity remain to be addressed and analysed more deeply. By addressing a series of previously reported inventories of marine gastropod communities along a sharp gradient of pollution along southern coast at Suva (Fiji Archipelago), I first confirm the already recognised trend towards both a severe decrease in species richness and a strong increase of the unevenness in species abundance distribution, as a response to incremental pollution. Yet, the last trend – increased unevenness – reveals being essentially the purely mathematical consequence of the concomitant decline in species richness. In fact, the genuine intensity of the process of hierarchical structuring of species abundances proves remaining virtually unaffected by environmental degradation, contrary to what has been generally thought so far. Also, another unexpected aspect of the decline in species richness with growing pollution is that this decline is far from being primarily restricted to the set of rarest species; in fact, the originally abundant species are also largely implied in this decline. Moreover, considering separately the two co-occurring feeding guilds, it is shown that herbivores and carnivores are substantially involved the same in the drop in species diversity; as a result, their relative contributions in the community do not seem markedly contrasted by growing pollution. In another respect, a recently proposed paradigmatic hypothesis is supported, according to which the herbivore-guild has quite less numerous species with more unevenly distributed abundances, as compared to the carnivore-guild. Yet, once again, this increased unevenness is essentially the purely mathematical consequence of the concomitant decline in species richness; the genuine intensity of the process of hierarchical structuring of species abundances does remain substantially unchanged. At last, a comparatively extremely high sensitivity to pollution is highlighted for the emblematic genus Conus, which suffers, here, a dramatic drop in species diversity.
Antioxidant activities and phenolic composition of extracts from Greek oregano, Greek sage, and summer savory.

Oregano vulgare L. ssp. hirtum (Greek oregano), Salvia fruticosa (Greek sage), and Satureja hortensis (summer savory) were examined as potential sources of phenolic antioxidant compounds. The antioxidant capacities (antiradical activity by DPPH* test, phosphatidylcholine liposome oxidation, Rancimat test) and total phenol content were determined in the ethanol and acetone extracts of the dried material obtained from the botanically characterized plants. The ground material was also tested by the Rancimat test for its effect on the stability of sunflower oil. The data indicated that ground material and both ethanol and acetone extracts had antioxidant activity. Chromatographic (TLC, RP-HPLC) and NMR procedures were employed to cross-validate the presence of antioxidants in ethanol and acetone extracts. The major component of all ethanol extracts was rosmarinic acid as determined by RP-HPLC and NMR. Chromatography indicated the presence of other phenolic antioxidants, mainly found in the acetone extracts. The presence of the flavones luteolin and apigenin and the flavonol quercetin was confirmed in the majority of the extracts by the use of a novel (1)H NMR procedure, which is based on the strongly deshielded OH protons in the region of 12-13 ppm without previous chromatographic separation. This deshielding may be attributed to the strong intramolecular six-membered ring hydrogen bond of the OH(5). CO(4) moiety.
A learning-based approach for automatic image and video colorization

In this paper, we present a color transfer algorithm to colorize a broad range of gray images without any user intervention. The algorithm uses a machine learning-based approach to automatically colorize grayscale images. The algorithm uses the superpixel representation of the reference color images to learn the relationship between different image features and their corresponding color values. We use this learned information to predict the color value of each grayscale image superpixel. As compared to processing individual image pixels, our use of superpixels helps us to achieve a much higher degree of spatial consistency as well as speeds up the colorization process. The predicted color values of the gray-scale image superpixels are used to provide a 'micro-scribble' at the centroid of the superpixels. These color scribbles are refined by using a voting based approach. To generate the final colorization result, we use an optimization-based approach to smoothly spread the color scribble across all pixels within a superpixel. Experimental results on a broad range of images and the comparison with existing state-of-the-art colorization methods demonstrate the greater effectiveness of the proposed algorithm.