Miracle-dz/UniFAR-FTUs huggingface dataset:
Aryl Hydrocarbon Receptor Regulates Distinct Dioxin-Dependent and Dioxin-Independent Gene Batteries

Conventional biochemical and molecular techniques identified previously several genes whose expression is regulated by the aryl hydrocarbon receptor (AHR). We sought to map the complete spectrum of AHR-dependent genes in male adult liver using expression arrays to contrast mRNA profiles in Ahr-null mice (Ahr–/–) with those in mice with wild-type AHR (Ahr+/+). Transcript profiles were determined both in untreated mice and in mice treated 19 h earlier with 1000 μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression of 456 ProbeSets was significantly altered by TCDD in an AHR-dependent manner, including members of the classic AHRE-I gene battery, such as Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1. In the absence of exogenous ligand, AHR status alone affected expression of 392 ProbeSets, suggesting that the AHR has multiple functions in normal physiology. In Ahr–/– mice, only 32 ProbeSets exhibited responses to TCDD, indicating that the AHR is required for virtually all transcriptional responses to dioxin exposure in liver. The flavin-containing monooxygenases, Fmo2 and Fmo3, considered previously to be uninducible, were highly induced by TCDD in an AHR-dependent manner. The estrogen receptor α as well as two estrogen-receptor-related genes (α and γ) exhibit AHR-dependent expression, thereby extending cross-talk opportunities between the intensively studied AHR and estrogen receptor pathways. p53 binding sites are over-represented in genes down-regulated by TCDD, suggesting that TCDD inhibits p53 transcriptional activity. Overall, our study identifies a wide range of genes that depend on the AHR, either for constitutive expression or for response to TCDD.
Inhibition by dietary selenium of colon cancer induced in the rat by bis(2-oxopropyl)nitrosamine.

Abstract Wistar-derived MRC rats were fed casein diets supplemented with 0.1 or 2.0 ppm selenium as sodium selenite from 7 weeks of age. At 8 weeks, weekly injections (5 mg/kg body weight s.c.) of bis(2-oxopropyl)nitrosamine (BOP) were started. Rats were killed after 50 injections; blood samples were collected after 1, 10, 25, and 50 weeks; and tissue samples were retained at killing for measuring hematology and selenium status. Carcinogen treatment did not influence body weight or survival. The high selenium level reduced female growth and improved male survival. Hemoglobin was reduced and mean corpuscular volume was increased in both sexes by feeding high-selenium diets. In addition, white blood cell counts were increased in BOP-treated males. Blood, liver, pancreas, and kidney selenium rose in rats fed the high-selenium diets. BOP treatment reduced liver selenium at the low dietary level and increased pancreas selenium at the high level. Glutathione peroxidase values in erythrocytes and plasma increased with the high-selenium diets, whereas its activity in the liver was not influenced by dietary selenium but was reduced in male rats by BOP treatment. Colon adenocarcinoma yield was reduced in male rats fed the high selenium level (16 carcinomas in 30 rats) by comparison with the low selenium level (28 carcinomas in 29 rats). Lung adenocarcinoma incidence decreased to none in 30 male rats fed the high-selenium diet from 4 in 29 male rats (14%) given the low selenium level. Female rats did not develop colon or lung adenocarcinomas at either selenium level. The influence of dietary selenium in the colon was related to an increased repair rate of BOP-induced DNA damage in this tissue.
System Utilization of Large-Scale Integration

A new approach to a computer organization promises very effective utilization of the LSI technology. Functional partitioning of both the data path and control is employed. A dramatic reduction in array pin requirements by a factor of two or more is achieved. Arrays as small as a few dozen gates can be effectively utilized. The total system is exceedingly flexible in both performance and instruction set.
Towards an Author-Topic-Term-Model Visualization of 100 Years of German Sociological Society Proceedings

Author co-citation studies employ factor analysis to reduce high-dimensional co-citation matrices to low-dimensional and possibly interpretable factors, but these studies do not use any information from the text bodies of publications. We hypothesise that term frequencies may yield useful information for scientometric analysis. In our work we ask if word features in combination with Bayesian analysis allow well-founded science mapping studies. This work goes back to the roots of Mosteller and Wallace's (1964) statistical text analysis using word frequency features and a Bayesian inference approach, tough with different goals. To answer our research question we (i) introduce a new data set on which the experiments are carried out, (ii) describe the Bayesian model employed for inference and (iii) present first results of the analysis.
Improving large graph processing on partitioned graphs in the cloud

As the study of large graphs over hundreds of gigabytes becomes increasingly popular for various data-intensive applications in cloud computing, developing large graph processing systems has become a hot and fruitful research area. Many of those existing systems support a vertex-oriented execution model and allow users to develop custom logics on vertices. However, the inherently random access pattern on the vertex-oriented computation generates a significant amount of network traffic. While graph partitioning is known to be effective to reduce network traffic in graph processing, there is little attention given to how graph partitioning can be effectively integrated into large graph processing in the cloud environment. In this paper, we develop a novel graph partitioning framework to improve the network performance of graph partitioning itself, partitioned graph storage and vertex-oriented graph processing. All optimizations are specifically designed for the cloud network environment. In experiments, we develop a system prototype following Pregel (the latest vertex-oriented graph engine by Google), and extend it with our graph partitioning framework. We conduct the experiments with a real-world social network and synthetic graphs over 100GB each in a local cluster and on Amazon EC2. Our experimental results demonstrate the efficiency of our graph partitioning framework, and the effectiveness of network performance aware optimizations on the large graph processing engine.
A Minimal Variance Estimator for the Cardinality of Big Data Set Intersection

In recent years there has been a growing interest in developing "streaming algorithms" for efficient processing and querying of continuous data streams. These algorithms seek to provide accurate results while minimizing the required storage and the processing time, at the price of a small inaccuracy in their output. A fundamental query of interest is the intersection size of two big data streams. This problem arises in many different application areas, such as network monitoring, database systems, data integration and information retrieval. In this paper we develop a new algorithm for this problem, based on the Maximum Likelihood (ML) method. We show that this algorithm outperforms all known schemes in terms of the estimation's quality (lower variance) and that it asymptotically achieves the optimal variance.
A study on automated segmentation of blood regions in Wireless Capsule Endoscopy images using fully convolutional networks

Wireless Capsule Endoscopy (WCE) is a novel diagnostic modality of endoscopic imaging which facilitates direct visualization of the gastrointestinal (GI) tract. Many computational methods that can automatically detect and/or characterize the abnormalities from WCE sequences are developed to support medical decision-making. This paper presents a new approach for automated segmentation of blood regions in WCE images via a deep learning strategy. The proposed method first classify the bleeding samples into active and inactive subgroups based on the statistical features derived from the histogram probability of the color space. Then for each subgroup, we highlight the blood regions via fully convolutional networks (FCNs). Experimental results on the clinical WCE dataset demonstrate the efficacy of our approach, which achieves comparable or better performance than the state-of-the-art methods.
A distance‐dependent atomic knowledge‐based potential for improved protein structure selection

A heavy atom distance‐dependent knowledge‐based pairwise potential has been developed. This statistical potential is first evaluated and optimized with the native structure z‐scores from gapless threading. The potential is then used to recognize the native and near‐native structures from both published decoy test sets, as well as decoys obtained from our group's protein structure prediction program. In the gapless threading test, there is an average z‐score improvement of 4 units in the optimized atomic potential over the residue‐based quasichemical potential. Examination of the z‐scores for individual pairwise distance shells indicates that the specificity for the native protein structure is greatest at pairwise distances of 3.5–6.5 Å, i.e., in the first solvation shell. On applying the current atomic potential to test sets obtained from the web, composed of native protein and decoy structures, the current generation of the potential performs better than residue‐based potentials as well as the other published atomic potentials in the task of selecting native and near‐native structures. This newly developed potential is also applied to structures of varying quality generated by our group's protein structure prediction program. The current atomic potential tends to pick lower RMSD structures than do residue‐based contact potentials. In particular, this atomic pairwise interaction potential has better selectivity especially for near‐native structures. As such, it can be used to select near‐native folds generated by structure prediction algorithms as well as for protein structure refinement. Proteins 2001;44:223–232. © 2001 Wiley‐Liss, Inc.
Periscope: a system for adaptive 3D visualization of search results

A system for efficient 3D visualization of Web search results is presented. The system, called Periscope1, uses a novel approach for adaptive and customizable visualization of complex data. The whole process is divided into a number of interactive steps. At each step, the system can automatically choose the best method of presenting search results. The user can also select a specific presentation method to focus on certain properties of the result obtained. After analyzing the current search result, the user can narrow or broaden the search query and repeat the procedure.
POLITICAL SETTLEMENTS: Implications for International Development Policy and Practice

The Asia Foundation is a non-profit, non-governmental organization committed to the development of a peaceful, prosperous, just, and open Asia-Pacific region. The Foundation Asian initiatives to improve governance, law, and civil society; women's empowerment; economic reform and development; sustainable development and the environment; and international relations. Drawing on nearly 60 years of experience in Asia, the Foundation collaborates with private and public partners to support leadership and institutional development, exchanges, and policy research. Through Occasional Papers, The Asia Foundation presents a range of views on major political, economic, and security challenges facing the Asia-Pacific. The views expressed in this occasional paper are those of the author(s) and do not necessarily represent those of The Asia Foundation. ACKNOWLEDGEMENTS The authors would like to thank the following people for their invaluable advice, input, and support in the development of this paper: EXECUTIVE SUMMARY The process of development is fundamentally shaped by powerful political, economic, and security actors in aid-recipient countries. These actors use their influence to proactively shape and control formal governance institutions, policies, and the distribution of development assistance to advance their interests. The political settlements framework is an important new approach for international development organizations to better understand and respond to this reality and the challenges that result from political dynamics in developing countries. This framework allows policy makers and development practitioners to understand how development is driven by competition among elite groups, as an alternative to development approaches that focus on capacity-building or technical assistance. The term " political settlement " is commonly used to describe the informal power arrangements or " social order " in a country. The key elements of a political settlement are actors, interests, and institutions. In most cases, it is a coalition of powerful elite factions that make up the key actors in a political settlement. The critical element that holds a political settlement together is the alignment of interests within the dominant elite coalition, and the dynamic relationship between elite interests and the broader array of interests in the society. Institutions are viewed as malleable – as the product of ongoing conflict, negotiation, and compromise among powerful groups, with the ruling coalition shaping and controlling this process. In most cases, power relations are fluid and dynamic, and political settlements are constantly adapting and subject to renegotiation and contestation. As a result, political settlements should not be interpreted as one-time events, but rather as …
Olive Tree (Olea europeae L.) Leaves: Importance and Advances in the Analysis of Phenolic Compounds

Phenolic compounds are becoming increasingly popular because of their potential role in contributing to human health. Experimental evidence obtained from human and animal studies demonstrate that phenolic compounds from Olea europaea leaves have biological activities which may be important in the reduction in risk and severity of certain chronic diseases. Therefore, an accurate profiling of phenolics is a crucial issue. In this article, we present a review work on current treatment and analytical methods used to extract, identify, and/or quantify phenolic compounds in olive leaves.
Folded Compact Ultra-Wideband Stepped-Impedance Resonator Filters

New ultra-wideband stepped-impedance resonator configurations are presented which, in cascaded and folded forms, are well suited for compact small-size filter applications. Compared to similar structures known hitherto, improved stopband performance is obtained by structural folding and source-load coupling. A variety of different filter configurations is presented with bandwidths up to 105 percent covering the 3.1-10.6 GHz range. Excellent stopband performance is obtained up to 16 GHz. The filters are designed for standard microstrip applications on commonly used substrate materials, and their responses are verified by different commercial electromagnetic software packages.
Epithelial Electrolyte Transport Physiology and the Gasotransmitter Hydrogen Sulfide

Hydrogen sulfide (H2S) is a well-known environmental chemical threat with an unpleasant smell of rotten eggs. Aside from the established toxic effects of high-dose H2S, research over the past decade revealed that cells endogenously produce small amounts of H2S with physiological functions. H2S has therefore been classified as a “gasotransmitter. ” A major challenge for cells and tissues is the maintenance of low physiological concentrations of H2S in order to prevent potential toxicity. Epithelia of the respiratory and gastrointestinal tract are especially faced with this problem, since these barriers are predominantly exposed to exogenous H2S from environmental sources or sulfur-metabolising microbiota. In this paper, we review the cellular mechanisms by which epithelial cells maintain physiological, endogenous H2S concentrations. Furthermore, we suggest a concept by which epithelia use their electrolyte and liquid transport machinery as defence mechanisms in order to eliminate exogenous sources for potentially harmful H2S concentrations.
COQ2 polymorphisms are not associated with increased risk of statin-induced myalgia/myopathy in the Czech population

Abstract Background: The gene COQ2, encoding 4-hydroxybenzoate-polyprenyltransferase (coenzyme Q2), belongs to the candidates potentially influencing statin treatment tolerability. This enzyme is involved in the biosynthesis of coenzyme Q10 (CoQ10), in which depletion induced by statin treatment is implicated in the development of statin-associated muscle symptoms (SAMS). Thus, polymorphisms in the COQ2 gene might explain susceptibility to SAMS. Methods: Adult patients with SAMS (on low doses of atorvastatin and simvastatin)-induced myalgia/myopathy (n=278), patients on statins but without SAMS (n=293) and population (part of the post-MONICA [Multinational MONItoring of trends and determinants in CArdiovascular disease] study) controls (n=561) were genotyped (polymerase chain reaction-restriction fragment length polymorphism [PCR-RFLP] assay) for rs6535454 and rs4693075 polymorphisms within the COQ2 gene loci. Results: Distribution of rs6535454 in patients with SAMS (GG=51.1%, GA=40.0%, AA=8.9%) did not significantly differ (p=0.33; respectively 0.32 for codominant models of the analysis) from that in the population controls (GG=48.1%, GA=45.0%, AA=6.9%) or the SAMS-unaffected patients (GG=49.8%, GA=40.3%, AA=9.7%). Similarly, neither rs4693075 was associated with SAMS (CC=36.8%, CG=48.2%, GG=15.0% in patients suffering SAMS vs. CC=36.6%, CG=47.5%, GG=15.9 in controls and CC=35.8%, CG=48.2%, GG=15.9% in symptom-free patients, p=0.94 and 0.95 for codominant models of the analysis). Also, the haplotype distributions were not significantly different between the groups analyzed. Conclusions: The polymorphisms of the COQ2 gene do not associate with SAMS in the Czech patients treated with low doses of statins. This is another clue that the coenzyme Q10 pathway is not the most important for the development of SAMS.
Dcc Regulates Asymmetric Outgrowth of Forebrain Neurons in Zebrafish

The guidance receptor DCC (deleted in colorectal cancer) ortholog UNC-40 regulates neuronal asymmetry development in Caenorhabditis elegans, but it is not known whether DCC plays a role in the specification of neuronal polarity in vertebrates. To examine the roles of DCC in neuronal asymmetry regulation in vertebrates, we studied zebrafish anterior dorsal telencephalon (ADt) neuronal axons. We generated transgenic zebrafish animals expressing the photo-convertible fluorescent protein Kaede in ADt neurons and then photo-converted Kaede to label specifically the ADt neuron axons. We found that ADt axons normally project ventrally. Knock down of Dcc function by injecting antisense morpholino oligonucleotides caused the ADt neurons to project axons dorsally. To examine the axon projection pattern of individual ADt neurons, we labeled single ADt neurons using a forebrain-specific promoter to drive fluorescent protein expression. We found that individual ADt neurons projected axons dorsally or formed multiple processes after morpholino knock down of Dcc function. We further found that knock down of the Dcc ligand, Netrin1, also caused ADt neurons to project axons dorsally. Knockdown of Neogenin1, a guidance receptor closely related to Dcc, enhanced the formation of aberrant dorsal axons in embryos injected with Dcc morpholino. These experiments provide the first evidence that Dcc regulates polarized axon initiation and asymmetric outgrowth of forebrain neurons in vertebrates.
Identification of Genes with Differential Expression in Acquired Drug-Resistant Gastric Cancer Cells Using High-Density Oligonucleotide Microarrays

Purpose: A major obstacle in chemotherapy is treatment failure due to anticancer drug resistance. The emergence of acquired resistance results from host factors and genetic or epigenetic changes in the cancer cells. The purpose of this study was to identify differentially expressed genes associated with acquisition of resistance in human gastric cancer cells. Experimental Design: We performed global gene expression analysis in the acquired drug-resistant gastric cancer cell lines to the commonly used drugs 5-fluorouracil, doxorubicin, and cisplatin using Affymetrix HG-U133A microarray. The gene expression patterns of 10 chemoresistant gastric cancer cell lines were compared with those of four parent cell lines using fold-change and Wilcoxon’s test for data analysis. Results: We identified over 250 genes differentially expressed in 5-fluorouracil-, cisplatin-, or doxorubicin-resistant gastric cancer cell lines. Our expression analysis also identified eight multidrug resistance candidate genes that were associated with resistance to two or more of the tested chemotherapeutic agents. Among these, midkine (MDK), a heparin-binding growth factor, was overexpressed in all drug-resistant cell lines, strongly suggesting that MDK might contribute to multidrug resistance in gastric cancer cells. Conclusions: Our investigation provides comprehensive gene information associated with acquired resistance to anticancer drugs in gastric cancer cells and a basis for additional functional studies.
Rapid Deployment with Confidence: Calibration and Fault Detection in Environmental Sensor Networks

Rapidly deployable sensor networks are portable, reusable, and can take advantage of a human user in the field attending to the deployment. Unfortunately, even small disruptions or problems in collected data must be addressed quickly, as the overall quantity of data gathered is small relative to longterm deployments. In this paper we describe a procedure for calibration and a system for online fault remediation. Care in the calibration process for ion selective electrodes used for water quality assists interpretation of the data. Scientists will have more confidence in the data obtained from a rapid deployment if in-field users can detect and compensate for problems as they occur. We have designed and implemented a tool for use in the field to detect potential faults and provide actions to remedy or validate the faulty data. In January of 2006 we deployed 48 sensors over a period of 12 days in Bangladesh in order to aid in validating a hypothesis on the mass presence of arsenic in the groundwater. Our system is based on the the approximately 25,000 measurements we collected.
Mood and Stock Market Returns : International Evidence

We employ recent data from 59 international emerging and mature stock markets to provide new evidence of a lunar cycle (full and new moon) effect on their stock market returns. Using a TGARCH model, we further examine the linkages between efficient-market theory, calendar-related effects and investors' mood resulted from moon phases. The empirical results show significant full moon effects in 6 markets, and significant new moon effects in 8 markets. In line with the theory, we report significant positive effect of new moon on stock market returns in 5 cases (UK, Switzerland, Bangladesh, Chile and Cyprus), while a negative effect of full moon is reported for the case of Jordan only. In addition, we find that lunar effects are strongly influenced by the calendar anomalies (Monday effect and January effect); several markets -mostly emerging marketsshow evidence of full/new moon effects as well as Monday/January effects (Bangladesh, Brazil, Chile, Tunisia, Belgium, Cyprus). Further, we prove that the lunar phases are stronger outside America. These findings are recommended to investors, financial managers and analysts dealing with international stock indices.