Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human Papillomavirus Type 16 E6 Oncogene Regulates microRNA-218 via the Histone Acetyltransferase p300 in Cervical Carcinoma Cells

Human papillomaviruses (HPVs) are involved in the pathogenesis of different types of human cancers, especially cancer of the cervix (CaCx). MicroRNAs (miRNAs) are post-transcriptional gene regulators that have recently been associated with many types of cancers. We analyzed the expression of cellular miRNAs in HPV-16 positive cervical cell lines and tissues via microarray, Northern blotting, and quantitative RT-PCR. Three miRNAs were overexpressed and 24 underexpressed in cervical cell lines containing integrated HPV-16 DNA compared to the normal cervix. An HPV-negative CaCx cell line, C-33A, showed underexpression of four miRNAs compared to the normal cervix. Also, nine miRNAs were overexpressed and only one underexpressed in cell lines containing integrated HPV-16 DNA compared to C-33A. MicroRNA-218 (miR-218) was specifically underexpressed in cell lines, cervical lesions and cancer tissues containing integrated HPV-16 DNA compared to both C-33A and the normal cervix. Exogenous expression of the HPV-16 E6 oncogene reduced miR-218 expression, and conversely, RNA interference of E6/E7 oncogenes in an HPV-16 positive cell line increased miR-218 expression. Furthermore, exogenous expression of miR-218 in HPV-16 positive cell lines decreased expression of the epithelial-specific gene LAMB3, which is involved in cell migration and tumorigenicity. We analyzed the expression of cellular miRNAs in additional clinical samples including six HPV-16 positive cervical cancers, three cervical dysplasias, and four normal cervical tissues using TaqMan® MicroRNA Arrays V2.0. Eighteen miRNAs were overexpressed and two underexpressed in cervical cancer tissues compared to normal cervical tissues. Nine miRNAs were consistently overexpressed, and two miRNAs were consistently underexpressed, including miR-218, in cervical dysplasias and cervical cancer tissues compared to normal tissues. We also found that exogenous expression of miR-218 in HPV-16 positive cell lines decreased expression of the extracellular matrix protein MMP3, which is involved in the epithelial-mesenchymal transition. We also demonstrated that HPV-16 E6 regulates miR-218 via the histone acetyltransferase p300 in cervical cells. The expression of miR-218 was found to be reduced in HPV-negative cells upon p300 knock-down or p300 inhibition with anacardic acid, and expression of miR-218 was reactivated in HPV-16 positive cells upon EZH2 knock-down or inhibition with adenosine dialdehyde. Reactivation of miR-218 was enhanced upon treatment with a combination of 5-azacytidine, trichostatin A, and adenosine dialdehyde. We also demonstrated that miR-218 reduces the migration and invasion of SiHa cervical cancer cells, indicating that miR-218 functions as a tumor suppressor in cervical cancer and that it may have therapeutic value.
Scale-Dependent Associations of Band-Tailed Pigeon Counts at Mineral Sites

Abstract The abundance of Band-tailed Pigeons (Patagioenas fasciata monilis) has declined substantially from historic numbers along the Pacific Coast. Identification of patterns and causative factors of this decline are hampered because habitat use data are limited, and temporal and spatial variability patterns associated with population indices are not known. Furthermore, counts are influenced not only by pigeon abundance but also by rate of visitation to mineral sites, which may not be consistent. To address these issues, we conducted mineral site counts during 2001 and 2002 at 20 locations from 4 regions in the Pacific Northwest, including central Oregon and western Washington, USA, and British Columbia, Canada. We developed inference models that consisted of environmental factors and spatial characteristics at multiple spatial scales. Based on information theory, we compared models within a final set that included variables measured at 3 spatial scales (0.03 ha, 3.14 ha, and 7850 ha). Pigeon counts increased from central Oregon through northern Oregon and decreased into British Columbia. After accounting for this spatial pattern, we found that pigeon counts increased 12% ± 2.7 with a 10% increase in the amount of deciduous forested area within 100 m from a mineral site. Also, distance from the mineral site of interest to the nearest known mineral site was positively related to pigeon counts. These findings provide direction for future research focusing on understanding the relationships between indices of relative abundance and complete counts (censuses) of pigeon populations by identifying habitat characteristics that might influence visitation rates. Furthermore, our results suggest that spatial arrangement of mineral sites influences Band-tailed Pigeon counts and the populations which those counts represent.
Lessons from forest decentralization: money, justice and the quest for good governance in Asia-Pacific.

Foreword M.S. Kaban 1. Setting the Stage: Money and Justice in Asian and Pacific Forests Carol J. Pierce Colfer, Ganga Ram Dahal and Moira Moeliono 2. From Decentralization to Governance: Recurring Issues Christian Kuchli 3. Governance, Tenure and Equity in Asia-Pacific Forests Lesley Potter 4. A Different Vantage Point: Decentralization, Women's Organizing and Local Forest Management Seema Arora-Jonsson 5. Community Forestry in Nepal: Decentralized Forest Governance Ganga Ram Dahal and Apsara Chapagain 6. Policies and Programme to Make Decentralization Effective: A Case Study from China Liu Dachang 7. Forest Fire Management and Autonomy in the Republic of Korea Byoung Il Yoo 8. The Gap between Policy and Practice in Lao PDR Yayoi Fujita and Kaisone Phengsopha 9. Consultative Planning for Effective Forest Governance: Case Studies from Malaysia and Indonesia Efransjah, Petrus Gunarso, Che Hashim bin Hassan and Kresno D. Santosa 10. Implementing Decentralization: Lessons from Experiences in Indonesia Kadjatmiko 11. Devolved and Decentralized Forest Management in the Philippines: Triggers and Constraints in Investments Ernesto S. Guiang, Ferdinand Esguerra and Domingo Bacalla 12. The Household Economy and Decentralization of Forest Management in Vietnam Tan Quang Nguyen 13. Decentralization and Forest Governance in Asia and the Pacific: Trends, Lessons and Continuing Challenges Doris Capistrano Afterword Bob Fisher
Changes in the Alkaloid Content of Developing Fruits of Tomato (Lycopersicon esculentum Mill.)I. ANALYSES OF CULTIVARS AND MUTANTS WITH DIFFERENT RIPENING CHARACTERISTICS

Normal ripening red-, orangeand yellow-fruited cultivars of tomato showed similar patterns of fruit growth and tomatine accumulation to those of non-ripening mutants. In all fruits, the tomatine concentration declined continuously from an early stage although the absolute amount per fruit showed a biphasic pattern of accumulation and decline. The 'turning point' occurred at an earlier developmental stage in normal fruits than in mutants. Normal fruits also had a lower initial and higher final tomatine content than mutants on a per fruit basis although, on a unit weight basis, their initial concentration was higher and final concentration lower. Small, prematurely-ripened red fruits had alkaloid levels intermediate between large, unripe, green fruits and large, ripe, red fruits. It is concluded that growth and ripening processes may both contribute to the decline in fruit tomatine.
The action of muscles in swimming fish.

This review will focus on the mechanical performance of the trunk muscles of fish in relation to their important role in the generation of lateral undulations during swimming. In most fish, the different muscle fibre types are located in separate regions in the trunk (e.g. Boddeke, Slijper & Van der Stelt, 1959). This makes fish muscle particularly suitable for investigating how different fibre types are used during locomotion. Not only can the activity of homogeneous fibre bundles be detected fairly easily by electromyography (e.g. Bone, 1966), but bundles of fibres of the same type may also be isolated for mechanical experiments which mimic the in vivo activation and strain variation (e.g. Altringham & Johnston, 1990a). The following questions will be addressed in particular. First, a swimming fish produces waves of curvature along its trunk with its muscles. What is the nature of the associated net bending moments along the trunk and how much power is produced along the trunk (section 2)? Second, what are the mechanical properties of muscle fibres of fish and what is their efficiency (sections 3 and 4)? How are the muscle fibres at different positions in the trunk of a swimming fish recruited during various swimming modes? What is their in vivo work and power output (section 5)? Space limits do not allow consideration of the structural design of the myomeres, nor the complex innervation patterns of fish muscles.
The relationship between emotional appetite and bipolar features in obese and non-obese individuals

Objectives: It is known that many different positive and negative emotions can affect appetite and also, individuals who have bipolar features often have emotional fluctuations. In this study, it was aimed to investigate the relationship between emotional appetite and bipolar features in obese individuals. Methods: One hundred and ninety obese individuals who applied for bariatric surgery and 136 non-obese individuals were evaluated with Emotional Appetite Questionnaire (EMAQ), Beck- Depression Inventory (BDI), Beck-Anxiety Inventory (BAI) and The Temperament Evaluation of Memphis, Pisa, Paris and San-Diego Auto-questionnaire (TEMPS-A) in the study. Results: In obese individuals who applied for bariatric surgery, the frequency of bipolar disorder was found to be 2% and binge eating disorder (BED) frequency was 51.2%. It was found that scores of appetite in negative emotions were higher in obese individuals with BED compared to obese individuals and it was higher in obese individuals compared to normal weight individuals. Cyclothymic features explained 27.2%, 25.8% and 15.7% of scores of appetite in negative situations of obese individuals with BED, obese individuals without BED and normal weight individuals, respectively. Conclusions: As a result of this study, it can be concluded that scores of appetite in negative situations may be affected by cyclothymic features in obese individuals with BED, in obese and normal weight individuals. Depression and anxiety symptoms are effective factors in explaining scores of appetite in negative situations of obese individuals with BED, obese and normal weight individuals.
The technical potential of Great Britain to produce ligno‐cellulosic biomass for bioenergy in current and future climates

Process and empirical‐based models that describe lignocellulosic biomass yield of the perennial energy grass Miscanthus (MiscanFor©), short rotation coppice (SRC) trees and shrubs, poplar and willow (ForestGrowth‐SRC) and a number of short rotation forest trees (ESC‐CARBINE), were used to estimate the yield potential for current and future climates across Great Britain (GB). In current climates, modelled yields for all feedstock crops varied between 8.1 and 10.6 Mg dry weight (DW) ha−1 yr−1 with willow SRC and poplar SRF producing the lowest and highest yields respectively. For the medium emissions scenario (UKCP09) in 2050, mean yield for all feedstock crops varied between 7.6 and 12.7 Mg DW ha−1 yr−1 with willow SRC and poplar SRF once again the lowest and the highest recorded yields. There were clear geographical trends within GB. Miscanthus yield was higher than all others in the south‐west (13.1 Mg DW ha−1 yr−1), SRC willow and SRC poplar in the north‐west (12.1–15.8 Mg DW ha−1 yr−1) and in the midlands and south‐east, SRF poplar was the highest yielding (10.5–11.6 Mg DW ha−1 yr−1). These geographical trends changed little with climate out to 2050, with mean yield of each ‘best feedstock’ increasing from 12.7 to 14.2 Mg DW ha−1 yr−1. Out to 2050, SRC declined slightly and Miscanthus and SRF poplar increased as the ‘best feedstock’ option. Except for a few localized examples, only SRF poplar had a higher yield than SRC or Miscanthus. These data suggest that in current and future climates, lignocellulosic biomass plantation species can be selected and optimized for best yield performance in different regions of GB. This modelling framework provides a valuable starting‐point for which to test the performance of new genetic material, as this becomes available and parameterized for the models and socio‐economic scenarios that may impact on the bioenergy industry.
VARIATION OF SEX ALLOCATION AMONG EIGHT TAXA OF THE MIMULUS GUTTATUS SPECIES COMPLEX (SCROPHULARIACEAE)

Characters related to sex allocation and the mating system were studied in eight California taxa of the Mimulus guttatus complex: M. guttatus, M. nasutus, M. glaucescens, M. Tilingii, M. nudatus, M. laciniatus, M. platycalyx, and M. micranthus, ranked in approximate decreasing levels of outbreeding. Dry weights and lengths of floral parts, pollen and ovule number, and timing of stigmatic closure were measured on plants in the growth chamber. As percent of total flower weight, allocation to stamens and corollas was lowest in M. micranthus (28%), intermediate in M. platycalyx, M. Tilingii, and M. laciniatus (50%), and high in other taxa (60%). Among M. micranthus, M. platycalyx, and M. laciniatus, pollen-ovule ratios ranged from 3.9 to 12.0; ratios for other taxa were 19.3 to 26.6. Taxa with increased male biomass allocation generally show increased outcrossing and increased P/O ratios. Stigma-anther separation and closure of stigma lobes upon touch were positively correlated with outcrossing ratios, P/O ratios, and male allocation. Isozyme variation indicates the inbreeding taxa have been independently derived; thus, these associations of maleness with outbreeding are significant trends in the Mimulus guttatus complex. HERMAPHRODITIC FLOWERS serve both male and female functions. In hermaphroditic-flowered species with higher selfing rates, the theory of local mate competition predicts increased allocation of resources to floral structures that are female in function (Charnov, 1979; Charlesworth and Charlesworth, 1981). The exact nature of this relationship is undetermined (Charnov, 1987), and more fundamentally, the gender of individual floral structures is subject to dispute (Cruden and Miller-Ward, 1981; Goldman and Willson, 1986). Some parts of the hermaphroditic flower, such as the anthers, pollen, pistils and ovules, are of unequivocal gender, while others, such as the corolla and the calyx, are not. However, if few pollinator visits are sufficient to fertilize almost all eggs while many pollinator visits are required to disperse pollen to other plants, the corolla should be predominantly male (Bell, 1985). In contrast, the calyx, with its permanent attachment to the ovary and its role in seed production and dispersal, has characteristics that are more female. Besides the prob
Squalenoyl Gemcitabine Monophosphate: Synthesis, Characterisation of Nanoassemblies and Biological Evaluation

Trialkylammonium 4-(N)-1,1',2-trisnor-squalenoylgemcitabine monophosphate (SQdFdC-MP) salts were prepared from 1,1',2-trisnor-squalenoylgemcitabine by phosphoramidite-type chemistry. This amphiphilic molecule self-assembled into nanoassemblies of about 100 nm in size in aqueous solutions. Cryo-TEM and small-angle X-ray scattering (SAXS) investigations revealed that SQdFdC-MP molecules self-organized into unilamellar liposomes with a membrane thickness of about 70 A. Such liposomal trialkylammonium SQdFdC-MP formulations displayed significant anticancer activity on leukaemia cells. These results suggested that squalene conjugates of negatively charged nucleotide analogues efficiently penetrated into tumour cells. Furthermore, triethylammonium SQdFdC-MP nanoassemblies were found to be more active than the parent nucleoside towards the L1210 10 K resistant cell line.
Short communication. Phytophthora nicotianae, the causal agent of root and crown rot (Tristeza disease) of red pepper in La Vera region (Cáceres, Spain)

Root and crown rot (Tristeza disease) is an increasing problem for red pepper crop in La Vera region (Caceres, western Spain). Field surveys were carried on in 2006 and 2007 to identify the causal agents of this disease. A Phytophthora species was isolated from diseased plants in most of the surveyed fields (27 of 36 in 2006 and 15 of 16 in 2007), while Verticillium spp. were not detected. Fifteen Phytophthora isolates were examined and identified as P. nicotianae, all of them were heterothalic isolates of mating type A2. Pathogenicity tests conducted on ‘Jaranda’ red pepper plants developed symptoms of wilt and root and crown rot, although disease severity differed significantly (P < 0.001) among isolates. Results indicate that P. nicotianae is the principal causal agent of the Tristeza disease of red pepper plants in La Vera region and this has several implications for the development of future disease management strategies. The host range of isolates from red pepper plants should be studied in order to establish suitable crop rotation in this region. Additional key words: ‘Jaranda’ cultivar, paprika, Phytophthora parasitica.
Contact problems based on the Penalty method

In this paper the contact problems including frictional effects are presented. Contact between two deformable bodies is considered in general. The present approach, based on the Coulomb's frictional law, elastic-plastic tangential slip decomposition and consistent linearization results in quadratic rates of convergence with the help of the Newton-Raphson iterative solution scheme. The results for the verification example are also presented.
A Variable Structure Controller Design of the Nonlinear System With Mismatched Uncertainties

The variable structure controller of a class of nonlinear systems with mismatched uncertainties is considered in this paper. The switching function is designed by solving the algebraic Riccati equation for the subsystem with mismatched uncertainties, and the corresponding variable structure control law is derived by realizable condition for the sliding-mode motions. Furthermore, a new adaptive variable structure controller is presented with the estimations for the upper norms of the uncertainties. The simulation result shows the validity of the proposed method.
Integrating Semantics Into Developmental Models of Morphology Learning

A key challenge in language acquisition is learning morphological transforms relating word roots to derived forms. Traditional unsupervised algorithms ﬁnd morphological patterns in sequences of phonemes, but struggle to distinguish valid segmentations from spurious ones because they ignore meaning. For example, a system that correctly discovers ”add /z/” as a valid morphological transform ( song - songs , year - years ) might incorrectly infer that ”add /ah.t/” is also valid ( mark - market , spear - spirit ). We propose that learners could avoid these errors with a simple semantic assumption: morphological transforms approximately preserve meaning. We extend an algorithm from Chan and Yang (2008) by integrating proximity in vector-space word embeddings as a criterion for valid transforms. On a corpus of child-directed speech, we achieve both higher accuracy and broader coverage than the purely phonemic approach, even in more developmentally plausible learning paradigms. Finally, we consider a deeper semantic assumption that could guide the acquisition of more abstract, human-like morphological understanding.
Substâncias tóxicas persistentes (STP) no Brasil

The present article presents an assessment of PTS in Brazil including polychlorinated biphenyls, polycyclic aromatic hydrocarbons, benzene hexachloride, aldrin, dieldrin, endrin, p,p,-DDT, p,p,DDE, p,p,-DDD, hexachlorocyclohexanes (a-HCH, b-HCH, g-HCH and d-HCH), endossulfan, heptachlor and pentachlorophenol. The data presented here are related to a survey of PTS levels in different environmental matrixes (soil, sediment, water, air, biota) and human tissues (milk, blood, human hair), according to the scope of the UNEP-GEF Regionally Based Assessment of PTSs. Potential sources were evaluated considering national products and imports, since most of the literature does not allow source identification. Finally, Brazilian legislation was updated.
Shapes in cells dynamic instabilities, morphology, and curvature in biological membranes

Esta tesis trata sobre la comprension de los mecanismos fisicos que dan forma a las entidades biologicas recubiertas por membranas, como los organulos celulares o los liposomas. Se estudian teoricamente varias formas que adquieren las membranas. Sistemas sencillos con anadidos diferentes que enriquecen la complejidad del sistema en cuestion. Sea el efecto dinamico en la forma de vesiculas oblongas o tubulares debido al anclaje de polimeros [. ]; la forma de tubos bifasicos periodicos; o el estudio microscopico de los mecanismos de generacion de curvatura por el anclaje de helices alta, todos ellos nos han permitido entender mejor la morfologia intracelular.
bnclassify: Learning Bayesian Network Classifiers

The bnclassify package provides state-of-the art algorithms for learning Bayesian network classifiers from data. For structure learning it provides variants of the greedy hill-climbing search, a well-known adaptation of the Chow-Liu algorithm and averaged one-dependence estimators. It provides Bayesian and maximum likelihood parameter estimation, as well as three naive-Bayes-specific methods based on discriminative score optimization and Bayesian model averaging. The implementation is efficient enough to allow for time-consuming discriminative scores on medium-sized data sets. bnclassify provides utilities for model evaluation, such as cross-validated accuracy and penalized log-likelihood scores, and analysis of the underlying networks, including network plotting via the Rgraphviz package. It is extensively tested, with over 200 automated tests that give a code coverage of 94%. Here we present the main functionalities, illustrate them with a number of data sets, and comment on related software.
Methodology for Measuring Distortions to Agricultural Incentives

This paper outlines the methodological issues associated with the task of measuring that actual delivered direct protection or taxation to individual agricultural industries, as well as the direct protection or anti-protection to non-agricultural sectors. It begins with a guide to what elements in principle could be measured. There are two key purposes of the distortion estimates being generated by this project are: 1) to provide a long annual time series of indicators showing the extent to which price incentives faced by farmers and food consumers have been distorted directly and indirectly by own-government policies in all major developing, transition and high-income countries, and hence for the world as a whole; and 2) to attribute the price distortion estimates for each farm product to specific border or domestic policy measures, so they can serve as inputs into various types of partial and general equilibrium economic models for estimating the effects of those various policies on such things as national and international agricultural markets, farm value added, income inequality, poverty, and national, regional and global welfare.