Miracle-dz/UniFAR-FTUs huggingface dataset:
The Antiangiogenic Activity of rPAI-123 Inhibits Vasa Vasorum and Growth of Atherosclerotic Plaque

Plaque vascularity has been implicated in its growth and stability. However, there is a paucity of information regarding the origin of plaque vasculature and the role of vasa vasorum in plaque growth. To inhibit growth of vasa vasorum in atherogenic mice and assess its effect on plaque growth, we used a truncated plasminogen activator inhibitor (PAI)-1 protein, rPAI-123, that has significant antiangiogenic activity. Female LDLR−/−ApoB-48–deficient mice fed Paigen’s diet without cholate for 20 weeks received rPAI-123 treatment (n=21) for the last 6 weeks. Plaque size and vasa vasorum density were compared to 2 controls: mice fed Paigen’s diet and treated with saline for the last 6 weeks (n=16) and mice fed Paigen’s diet until the onset of treatment (n=14). The rPAI-123 treatment significantly reduced plaque area and plaque cholesterol in the descending aorta and plaque area in the innominate artery. Measurements of reconstructed confocal microscopy images of vasa vasorum demonstrate that rPAI-123 treatment decreased vasa vasorum area and length, which was supported by microCT images. Confocal images provide evidence for vascularized plaque in the saline-treated group but not in rPAI-123–treated mice. The increased vessel density in saline-treated mice is attributable, in part, to upregulated fibroblast growth factor-2 expression, which is inhibited by rPAI-123. In conclusion, rPAI-123 inhibits growth of vasa vasorum, as well as vessels within the adjacent plaque and vessel wall, through inhibition of fibroblast growth factor-2, leading to reduced plaque growth in atherogenic female LDLR−/−ApoB-48–deficient mice.
Evaluation of mutagenic activity in an extract of pepper tree stem bark (Schinus terebinthifolius Raddi)

An extract (decoction) from pepper tree stem bark (Schinus terebinthifolius Raddi) is widely used in Brazil as a topical antiinflammatory agent and to cicatrize wounds. The extract contains catechin, tannins, terpenes, flavonoids, and saponins; of these components, both mutagenic potential and antioxidant properties have been ascribed to flavonoids. The mutagenicity of some flavonoids is believed to be associated with the formation of reactive oxygen species and seems to depend on the number and position of hydroxyl groups. In the present study, we evaluated an extract of S. terebinthifolius in a series of cell‐free and bacterial assays in order to determine its genotoxic potential. The extract was negative in a cell‐free plasmid DNA test, indicating that it did not directly break DNA. Positive results, however, were obtained in the SOS chromotest, in a forward mutagenesis assay employing CC104 and CC104mutMmutY strains of Escherichia coli, and in the Salmonella reversion assay, using strains TA97, TA98, TA100, and TA102. All the bacterial tests were performed without exogenous metabolic activation due to the topical use of this preparation. The results indicate that pepper tree stem bark extract produces DNA damage and mutation in bacteria, and that oxidative damage may be responsible for the genotoxicity. Environ. Mol. Mutagen. 42:185–191, 2003. © 2003 Wiley‐Liss, Inc.
Initial Identification of an Manganese Resistant Microorgnism

On the basis of the systematic investigation of manganese tolerating plants which grew in Xiangtan manganese tailings, rhizosphere soils of Chenopodiumalbum Linn were collected. 1 yellow manganese-resistant strain numbered XY was isolated from the rhizosphere of fresh plant through concentration gradient screening technique, and the cellular form, physiological and biochemical tests were conducted, as the growth curve and effects of temperature, pH, NaCl concentration to growth of the strain tested were investigated. The results of the tests showed that 1) the strain reached logarithmic phase in10-12h, 2) the optimal temperature range of the strain was35¡æ-40¡æ 3) the optimal pH range of the strain was 7.0-7.3;4) the optimal NaCl concentration range of the strain was10g/L. The status of the strain XY in the taxonomy and phylogeny has been conformed according to 16S rDNA sequences, the strain XY belongs to Planococcus genus.
On the Estimation of the Proportion of True Recent Infections Using the BED Capture Enzyme Immunoassay

In this short note, we analyze the assumptions made by McDougal et al (2006), both explicit and implicit, in their estimation of the proportion of "true recent infections" using the BED CEIA. This enables us to write down expressions for the sensitivity, short term specificity and long term specificity of a test for recent infection defined by a BED ODn below a threshold. We then derive an identity which shows the relationship between these parameters, allowing the elimination of sensitivity and short term specificity from an expression relating the proportion of "true recent infections" to the proportion of seropositive individuals testing below threshold. This has two important consequences. Firstly, the simplified formula is substantially more amenable to calibration. Secondly, naively treating the parameters as independent would lead to an incorrect estimate of uncertainty due to imperfect calibration.
SB: mmSystem - Using Decompositional Semantics for Lexical Simplification

In this paper, we describe the system we submitted to the SemEval-2012 Lexical Simplification Task. Our system (mmSystem) combines word frequency with decompositional semantics criteria based on syntactic structure in order to rank candidate substitutes of lexical forms of arbitrary syntactic complexity (one-word, multi-word, etc.) in descending order of (cognitive) simplicity. We believe that the proposed approach might help to shed light on the interplay between linguistic features and lexical complexity in general.
A GENERALIZED WILCOXON TEST FOR COMPARING ARBITRARILY SINGLY-CENSORED SAMPLES.

H2: F1(t) F2(t) (t F2(t) (t < T). The asymptotic efficiency of the test relative to the efficient parametric test when the distributions are exponential is at least 0 75 and increases with degree of censoring. When Ho is true, the test is not seriously affected by real differences in the percentage censored in the two groups. Some comparisons are made for five cases of varying degrees of censoring and tying between probabilities from the exact test and those from the proposed test and these suggest the test is appropriate under certain conditions when the sample size is five in each group. A worked example is presented and some discussion is given to further problems.
Antitumoral activity of allosteric inhibitors of protein kinase CK2

Introduction Due to its physiological role into promoting cell survival and its dysregulation in most cancer cells, protein kinase CK2 is a relevant physiopathological target for development of chemical inhibitors. We report the discovery of azonaphthalene derivatives, as a new family of highly specific CK2 inhibitors. First, we demonstrated that CK2 inhibition (IC50= 0.4 μM) was highly specific, reversible and non ATP-competitive. Small Angle X-ray Scattering experiments showed that this inhibition was due to large conformational change of CK2α upon binding of these inhibitors. We showed that several compounds of the family were cell-potent CK2 inhibitors promoting cell cycle arrest of human glioblastoma U373 cells. Finally, in vitro and in vivo assays showed that these compounds could decrease U373 cell tumor mass by 83% emphasizing their efficacy against these apoptosis-resistant tumors. In contrast, Azonaphthalene derivatives inactive on CK2 activity showed no effect in colony formation and tumor regression assays. These findings illustrate the emergence of nonclassical CK2 inhibitors and provide exciting opportunities for the development of novel allosteric CK2 inhibitors. Background CK2 is an emerging therapeutic target and ATP-competitive inhibitors have been identified. CK2 is endowed with specific structural features providing alternative strategies for inhibition. Results Azonaphthalene compounds are allosteric CK2 inhibitors showing antitumor activity. Conclusion CK2 may be targeted allosterically. Significance These inhibitors provide a foundation for a new paradigm for specific CK2 inhibition.
Larval and adult nutrition effects on blood/nectar choice of Culex nigripalpus mosquitoes

Abstract. The impact of nutritional variables on the development of host‐seeking and biting behaviours after emergence by female Culex nigripalpus mosquitoes were studied using air‐flow olfactometer and close‐range biting assays, respectively. Unfed females failed to develop resting stage ovarian follicles. When offered a bird host in the absence of competing stimuli, sugar‐fed mosquitoes were significantly more responsive in both host‐seeking and biting than unfed controls. In a choice olfactometer assay using nectar odours (honey scented with artificial apple‐blossom oil) versus host odours (a bird), unfed females preferred honey over bird odours except when honey odour was weak. After sucrose feeding, females switched from honey to bird preference. This change in behaviour was accompanied by significant accumulation of lipid and by follicular growth to the resting stage. Elevation of host responsiveness after sugar feeding was reversible; starvation ultimately resulted in females preferring honey over bird odours. When the larval diet was restricted by crowding, the wing‐length and total lipid of resultant adult females were reduced. Although differences were subtle, unfed bird‐responding females tended to have longer wings and more lipid than their honey‐responding counterparts.
Lep-MAP: fast and accurate linkage map construction for large SNP datasets

MOTIVATION Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses. RESULTS We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material. AVAILABILITY AND IMPLEMENTATION Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.
Complete Genome Sequence and In Planta Subcellular Localization of Maize Fine Streak Virus Proteins

ABSTRACT The genome of the nucleorhabdovirus maize fine streak virus (MFSV) consists of 13,782 nucleotides of nonsegmented, negative-sense, single-stranded RNA. The antigenomic strand consisted of seven open reading frames (ORFs), and transcripts of all ORFs were detected in infected plants. ORF1, ORF6, and ORF7 had significant similarities to the nucleocapsid protein (N), glycoprotein (G), and polymerase (L) genes of other rhabdoviruses, respectively, whereas the ORF2, ORF3, ORF4, and ORF5 proteins had no significant similarities. The N (ORF1), ORF4, and ORF5 proteins localized to nuclei, consistent with the presence of nuclear localization signals (NLSs) in these proteins. ORF5 likely encodes the matrix protein (M), based on its size, the position of its NLS, and the localization of fluorescent protein fusions to the nucleus. ORF2 probably encodes the phosphoprotein (P) because, like the P protein of Sonchus yellow net virus (SYNV), it was spread throughout the cell when expressed alone but was relocalized to a subnuclear locus when coexpressed with the MFSV N protein. Unexpectedly, coexpression of the MFSV N and P proteins, but not the orthologous proteins of SYNV, resulted in accumulations of both proteins in the nucleolus. The N and P protein relocalization was specific to cognate proteins of each virus. The subcellular localizations of the MFSV ORF3 and ORF4 proteins were distinct from that of the SYNV sc4 protein, suggesting different functions. To our knowledge, this is the first comparative study of the cellular localizations of plant rhabdoviral proteins. This study indicated that plant rhabdoviruses are diverse in genome sequence and viral protein interactions.
Shape Displays: Spatial Interaction with Dynamic Physical Form

Shape displays are an emerging class of devices that emphasize actuation to enable rich physical interaction, complementing concepts in virtual and augmented reality. The ability to render form introduces new opportunities to touch, grasp, and manipulate dynamic physical content and tangible objects, in both nearby and remote environments. This article presents novel hardware, interaction techniques, and applications, which point to the potential for extending the ways that we traditionally interact with the physical world, empowered by digital computation.
De relatie tussen employability en de intentie tot langer doorwerken

In Nederland hebben de sociale partners en de huidige regering besloten om in 2020 de pensioengerechtigde leeftijd te verhogen naar 66 jaar. Het wordt daarmee nog belang‐ rijker om te begrijpen wat werknemers motiveert om langer door te werken. In deze stu‐ die, onder 151 gemeenteambtenaren van 45 jaar en ouder, staat de vraag centraal in hoeverre het vergroten van hun employability samenhangt met hun intentie tot langer doorwerken. Ook is onderzocht in welke mate ‘leerwaarde van de functie’, ‘training en opleiding’, en ‘loopbaanmanagement’ een rol spelen bij hun verdere loopbaanontwikke‐ ling. Covariantiestructuuranalyses wezen uit dat naarmate deze werknemers hun employability hoger inschatten, ze een sterkere intentie hebben om langer door te wer‐ ken. Daarnaast blijken ‘leerwaarde van de functie’ en ‘training en opleiding in aangren‐ zende expertisegebieden’ belangrijke antecedenten te zijn van employabilitybevorde‐ ring. Er wordt geconcludeerd dat het voor de inzetbaarheid van oudere werknemers belangrijk is om functies zodanig in te richten dat ze uitdagend zijn en voldoende leer‐ mogelijkheden bevatten. Ook investeringen in een bredere ontwikkeling van oudere werknemers hangen positief samen met hun inzetbaarheid.
Individual entanglements in a simulated polymer melt.

We examine entanglements using monomer contacts between pairs of chains in a Brownian-dynamics simulation of a polymer melt. A map of contact positions with respect to the contacting monomer numbers (i,j) shows clustering in small regions of (i,j) which persists in time, as expected for entanglements. Using the ``space''-time correlation function of the aforementioned contacts, we show that a pair of entangled chains exhibits a qualitatively different behavior than a pair of distant chains when brought together. Quantitatively, about 50% of the contacts between entangled chains are persistent contacts not present in independently moving chains. In addition, we account for several observed scaling properties of the contact correlation function.
Rethinking Households: An Atomistic Perspective on European Living Arrangements

The study of living arrangements has been undertaken by various disciplines in the social sciences, such as family history, anthropology, demography and household economics. This resulted in independent formulations, often disparate and contradictory, the majority of which assume that household formation depends on a natural desire on the part of past populations to form complex households composed of married couples or parent-child groups from successive generations. In this present study Michel Verdon posits a radical and multidisciplinary method of examining household formation by refuting this 'collectivist set of suppositions' and recognizing residence as the critical determinant of all household forming practices. This book argues that the natural preference of adults not constituting part of a couple is to reside independently of others. The reasons why they do not do so are contingent on various economic or cultural constraints. The author has thoroughly surveyed the theoretical literature in the various disciplines and found it possible to unify all studies of living arrangements, be they of the past, the present and even the future, under one underlying 'atomistic set of suppositions'. Straddling the fields of anthropology and family history while borrowing key insights from household economics and demography, this book aims at dispelling a host of false assumptions in much of the literature on living arrangements while introducing a new framework for multidisciplinary communication and analysis.
CYB5D2 Requires Heme-Binding to Regulate HeLa Cell Growth and Confer Survival from Chemotherapeutic Agents

The cytochrome b5 domain containing 2 (CYB5D2; Neuferricin) protein has been reported to bind heme, however, the critical residues responsible for heme-binding are undefined. Furthermore, the relationship between heme-binding and CYB5D2-mediated intracellular functions remains unknown. Previous studies examining heme-binding in two cytochrome b5 heme-binding domain-containing proteins, damage-associated protein 1 (Dap1; Saccharomyces cerevisiae) and human progesterone receptor membrane component 1 (PGRMC1), have revealed that conserved tyrosine (Y) 73, Y79, aspartic acid (D) 86, and Y127 residues present in human CYB5D2 may be involved in heme-binding. CYB5D2 binds to type b heme, however, only the substitution of glycine (G) at D86 (D86G) within its cytochrome b5 heme-binding (cyt-b5) domain abolished its heme-binding ability. Both CYB5D2 and CYB5D2(D86G) localize to the endoplasmic reticulum. Ectopic CYB5D2 expression inhibited cell proliferation and anchorage-independent colony growth of HeLa cells. Conversely, CYB5D2 knockdown and ectopic CYB5D2(D86G) expression increased cell proliferation and colony growth. As PGRMC1 has been reported to regulate the expression and activities of cytochrome P450 proteins (CYPs), we examined the role of CYB5D2 in regulating the activities of CYPs involved in sterol synthesis (CYP51A1) and drug metabolism (CYP3A4). CYB5D2 co-localizes with cytochrome P450 reductase (CYPOR), while CYB5D2 knockdown reduced lanosterol demethylase (CYP51A1) levels and rendered HeLa cells sensitive to mevalonate. Additionally, knockdown of CYB5D2 reduced CYP3A4 activity. Lastly, CYB5D2 expression conferred HeLa cell survival from chemotherapeutic agents (paclitaxel, cisplatin and doxorubicin), with its ability to promote survival being dependent on its heme-binding ability. Taken together, this study provides evidence that heme-binding is critical for CYB5D2 in regulating HeLa cell growth and survival, with endogenous CYB5D2 being required to modulate CYP activities.
Improving Semantic Relevance for Sequence-to-Sequence Learning of Chinese Social Media Text Summarization

Current Chinese social media text summarization models are based on an encoder-decoder framework. Although its generated summaries are similar to source texts literally, they have low semantic relevance. In this work, our goal is to improve semantic relevance between source texts and summaries for Chinese social media summarization. We introduce a Semantic Relevance Based neural model to encourage high semantic similarity between texts and summaries. In our model, the source text is represented by a gated attention encoder, while the summary representation is produced by a decoder. Besides, the similarity score between the representations is maximized during training. Our experiments show that the proposed model outperforms baseline systems on a social media corpus.
Automatic Software Test Data Generation for Spanning Sets Coverage Using Genetic Algorithms

Software testing takes a considerable amount of time and resources spent on producing software. Therefore, it would be useful to have ways to reduce the cost of software testing. The new concepts of spanning sets of entities suggested by Marre and Bertolino are useful for reducing the cost of testing. In fact, to reduce the testing effort, the generation of test data can be targeted to cover the entities in the spanning set, rather than all the entities in the tested program. Marre and Bertolino presented an algorithm based on the subsumption relation between entities to find spanning sets for a family of control flow and data flow-based test coverage criteria. This paper presents a new general technique for the automatic test data generation for spanning sets coverage. The proposed technique applies to the algorithm proposed recently by Marre and Bertolino to automatically generate the spanning sets of program entities that satisfy a wide range of control flow and data flow-based test coverage criteria. Then, it uses a genetic algorithm to automatically generate sets of test data to cover these spanning sets. The proposed technique employed the concepts of spanning sets to limit the number of test cases, guide the test case selection, overcome the problem of the redundant test cases and automate the test path generation.
Machine learning algorithms for the creation of clinical healthcare enterprise systems

ABSTRACT Clinical recommender systems are increasingly becoming popular for improving modern healthcare systems. Enterprise systems are persuasively used for creating effective nurse care plans to provide nurse training, clinical recommendations and clinical quality control. A novel design of a reliable clinical recommender system based on multiple classifier system (MCS) is implemented. A hybrid machine learning (ML) ensemble based on random subspace method and random forest is presented. The performance accuracy and robustness of proposed enterprise architecture are quantitatively estimated to be above 99% and 97%, respectively (above 95% confidence interval). The study then extends to experimental analysis of the clinical recommender system with respect to the noisy data environment. The ranking of items in nurse care plan is demonstrated using machine learning algorithms (MLAs) to overcome the drawback of the traditional association rule method. The promising experimental results are compared against the sate-of-the-art approaches to highlight the advancement in recommendation technology. The proposed recommender system is experimentally validated using five benchmark clinical data to reinforce the research findings.