bluuebunny/crossref_metadata_2025 huggingface dataset:
Small-molecule agonists for the thyrotropin receptor stimulate thyroid function in human thyrocytes and mice
Authors: Neumann Susanne , Huang Wenwei , Titus Steve , Krause Gerd , Kleinau Gunnar , Alberobello Anna Teresa , Zheng Wei , Southall Noel T. , Inglese James , Austin Christopher P. , Celi Francesco S. , Gavrilova Oksana , Thomas Craig J. , Raaka Bruce M. , Gershengorn Marvin C.
Published: July 2009

Seven-transmembrane-spanning receptors (7TMRs) are prominent drug targets. However, small-molecule ligands for 7-transmembrane-spanning receptors for which the natural ligands are large, heterodimeric glycoprotein hormones, like thyroid-stimulating hormone (TSH; thyrotropin), have only recently been reported, and none are approved for human use. We have used quantitative high-throughput screening to identify a small-molecule TSH receptor (TSHR) agonist that was modified to produce a second agonist with increased potency. We show that these agonists are highly selective for human TSHR versus other glycoprotein hormone receptors and interact with the receptor's serpentine domain. A binding pocket within the transmembrane domain was defined by docking into a TSHR homology model and was supported by site-directed mutagenesis. In primary cultures of human thyrocytes, both TSH and the agonists increase mRNA levels for thyroglobulin, thyroperoxidase, sodium iodide symporter, and deiodinase type 2, and deiodinase type 2 enzyme activity. Moreover, oral administration of the agonist stimulated thyroid function in mice, resulting in increased serum thyroxine and thyroidal radioiodide uptake. Thus, we discovered a small molecule that activates human TSHR in vitro, is orally active in mice, and could be a lead for development of drugs to use in place of recombinant human TSH in patients with thyroid cancer.
Chimeric transcript discovery by paired-end transcriptome sequencing
Authors: Maher Christopher A. , Palanisamy Nallasivam , Brenner John C. , Cao Xuhong , Kalyana-Sundaram Shanker , Luo Shujun , Khrebtukova Irina , Barrette Terrence R. , Grasso Catherine , Yu Jindan , Lonigro Robert J. , Schroth Gary , Kumar-Sinha Chandan , Chinnaiyan Arul M.
Published: July 2009

Recurrent gene fusions are a prevalent class of mutations arising from the juxtaposition of 2 distinct regions, which can generate novel functional transcripts that could serve as valuable therapeutic targets in cancer. Therefore, we aim to establish a sensitive, high-throughput methodology to comprehensively catalog functional gene fusions in cancer by evaluating a paired-end transcriptome sequencing strategy. Not only did a paired-end approach provide a greater dynamic range in comparison with single read based approaches, but it clearly distinguished the high-level “driving” gene fusions, such as
BCR-ABL1
and
TMPRSS2-ERG
, from potential lower level “passenger” gene fusions. Also, the comprehensiveness of a paired-end approach enabled the discovery of 12 previously undescribed gene fusions in 4 commonly used cell lines that eluded previous approaches. Using the paired-end transcriptome sequencing approach, we observed read-through mRNA chimeras, tissue-type restricted chimeras, converging transcripts, diverging transcripts, and overlapping mRNA transcripts. Last, we successfully used paired-end transcriptome sequencing to detect previously undescribed ETS gene fusions in prostate tumors. Together, this study establishes a highly specific and sensitive approach for accurately and comprehensively cataloguing chimeras within a sample using paired-end transcriptome sequencing.
Population stability, cooperation, and the invasibility of the human species
Authors: Hamilton Marcus J. , Burger Oskar , DeLong John P. , Walker Robert S. , Moses Melanie E. , Brown James H.
Published: July 2009

The biogeographic expansion of modern humans out of Africa began ≈50,000 years ago. This expansion resulted in the colonization of most of the land area and habitats throughout the globe and in the replacement of preexisting hominid species. However, such rapid population growth and geographic spread is somewhat unexpected for a large primate with a slow, density-dependent life history. Here, we suggest a mechanism for these outcomes by modifying a simple density-dependent population model to allow varying levels of intraspecific competition for finite resources. Reducing intraspecific competition increases carrying capacities, growth rates, and stability, including persistence times and speed of recovery from perturbations. Our model suggests that the energetic benefits of cooperation in modern humans may have outweighed the slow rate of human population growth, effectively ensuring that once modern humans colonized a region long-term population persistence was near inevitable. Our model also provides insight into the interplay of structural complexity and stability in social species.
ETS family transcription factors collaborate with alternative signaling pathways to induce carcinoma from adult murine prostate cells
Authors: Zong Yang , Xin Li , Goldstein Andrew S. , Lawson Devon A. , Teitell Michael A. , Witte Owen N.
Published: July 2009

Chromosomal rearrangements involving erythroblast transformation specific (ETS) family transcription factors were recently defined as the most common genetic alterations in human prostate cancer. Despite their prevalence, it is unclear what quantitative role they play in either initiation or progression of the disease. Using a lentiviral transduction and dissociated cell prostate regeneration approach, we find that acutely increased expression of ETS proteins in adult murine prostate epithelial cells is sufficient to induce the formation of epithelial hyperplasia and focal prostatic intraepithelial neoplasia (PIN) lesions, but not progression to carcinoma. However, combined expression of ERG with additional genetic alternations associated with human prostate cancer can lead to aggressive disease. Although ERG overexpression does not cooperate with loss of the tumor suppressor p53, it does collaborate with alterations in PI3K signaling, such as Pten knockdown or AKT up-regulation, to produce a well-differentiated adenocarcinoma. Most striking is our finding that overexpression of androgen receptor (AR) does not give rise to any hyperplastic lesions, but when combined with high levels of ERG, it promotes the development of a more poorly differentiated, invasive adenocarcinoma. These findings suggest that in human prostate cancer, the most potent function of ETS gene fusions may be to synergize with alternative genetic events and provide different pathways for carcinoma production and invasive behavior. Our results provide direct evidence for selective cooperating events in ERG-induced prostate tumorigenesis and offer a rational basis for combined therapeutic interventions against multiple oncogenic pathways in prostate cancer.
Idiomatic false friends in English and Modern Standard Arabic
Authors: Al-Wahy Ahmed Seddik
Published: July 2009

This paper discusses idiomatic false friends (IFFs) in two genetically unrelated languages, English and Arabic. IFFs are defined as set phrases in two languages that have the same literal meaning but differ as regards their idiomatic meaning or their sociolinguistic and stylistic features. The study proposes a taxonomy for IFFs based on data from English and Arabic, though it may also apply to IFFs in other language pairs. In the case of English and Arabic, IFFs are either related (typically partial) or unrelated (typically total). Related IFFs have their origin in loan-translation, with idioms being borrowed from English into Arabic and then taking a different course of semantic development in each language. There are also cases in which the selection of a single sense of a polysemous idiom can be attributed to social and cultural factors. It is shown that, if idioms in general are among the most challenging units for translators, IFFs can be doubly difficult. The translator may assume that since the source and target language idioms have the same form, they can also have the same meaning or stylistic features.
Übersetzungstheorien und Gebrauchstexte
Authors: Simonnaes Ingrid
Published: July 2009

The central research question for this paper is how and to what extent translation theories affect the translation of legal texts. I will use the functional-pragmatic approach as one particular modern translation theory and investigate translation solutions in the field of lexical and syntactic problems on the basis of a small corpus of legal texts from the National translator’s exam. As a means of control I compare these solutions with suggested solutions of a small number of candidates preparing themselves for the exam and of some translation experts.

My findings show that the old dichotomy free vs. literal is not applicable to this type of translations as we find ourselves on a continuum. The translation brief and the legal force of a particular text influence strongly the translation strategy. Whenever the legal force of the source text supersedes the target text, the strategy of the translator should be at the ‘documentary’ (Nord 1989) end of the continuum. My findings need however to be corroborated on the basis of a much bigger corpus which for the time being is established at the Department of Professional and Intercultural Communication at the Norwegian School of Economics and Administration (NHH) including other language pairs than the one from which I have drawn my examples.
Social context and translation of public notices
Authors: Zhang Meifang
Published: July 2009

To study the translation of public notice is in effect seeking insights which take us beyond translation itself towards the whole relationship between language activity and the social context in which the translation is intended to function. Social context is an important aspect in the study of language and translation because the three are inextricably linked.

This paper attempts to investigate the text types, text functions and the translations of public notices functioning in the social context of Macao SAR of China. It tries to deduce about the contexts in which the ST and TT were produced, the purpose for which they were produced and the target reader for whom they were produced. The study is carried out in the light of Reiss’s theory of text typology (2000) and the Hallidayan systemic functional linguistics. It is hoped that this study will identity differences in public notice translation and explore the reasons behind the differences, and also be a test case for examining the role of functional theories of language in explaining some phenomena of translation.  Texts for the analysis are extracted from the database for a research project undertaken by the present writer, and the analysis is conducted in terms of three text types and functions: informative, expressive and operative. The results of this study reveal that although one of the language functions might be dominant in a single text in a public notice, overlapping or combining functions are very often bestowed upon most texts. They also show that although invariance in the transfer of content could be achieved in the translation of informative texts, and an analogous form in the translation could be found in the transfer of an expressive text, there are more differences than similarities in the translation of texts with operative functions.  Possible reasons behind the differences between the source and target texts are discussed. It is argued that the differences are most possibly caused by differences in cultural values, different religious backgrounds and different expectations between readers of the source and target texts.
Etymology and sememe analysis in translation
Authors: Hu Zhengmao
Published: July 2009

It is common to see various Chinese translations of a single English word/phrase in practice. Etymological tracing attempts to diachronically study the origin and its historical successive changes in both form and meaning of a given word/phrase, the purpose of which is acquisition of a comprehensive understanding of its core information. Sememe analysis is atomization of semantic components and deep semantic structure of both source language and target language to examine the semantic proximity and possible affinity between the two. This paper takes “stakeholder” and its Chinese translations as a case in point, for which there occurred a diplomatic and linguistic stir between the U. S. and China. By studying its origin, semantic evolution and dictionary definitions, and conducting a contrastive sememe analysis upon its various Chinese versions against the original word, this paper expounds the operationality of the qualitative method of etymological tracing and the quantitative one of sememe analysis and concludes that both etymological tracing and sememe analysis are viable approaches to tackling similar issues as seen in the case of “stakeholder”.
Teleworking and collaborative work environments in translation training
Authors: Olvera-Lobo María Dolores , Robinson Bryan , Senso José A. , Muñoz-Martín Ricardo , Muñoz-Raya Eva , Murillo-Melero Miguel , Quero-Gervilla Enrique , Castro-Prieto María Rosa , Conde-Ruano Tomás
Published: July 2009

The professional translation work is highly influenced by new communication opportunities, reason why teleworking must occupy its rightful
place in translator training at tertiary level. In addition, the ideal translation process should be divided into different stages (as
already occurs in major translation agencies), each task being assigned to a different team member with a different role. This paper
presents the results of a research study on translation students’ disposition towards and level of satisfaction with the use of a
collaborative work environment. We propose a “Professional Approach to Translator Training”, our didactic model combines elements of
roleplay, team-based task learning, simulation and case study in an innovative e-learning environment that functions via a collaborative
platform (BSCW).

Questionnaires were designed and used as evaluation tools before and after the experience of working in a collaborative environment. The
aim of these evaluation tools was to measure students’ knowledge of the following skills: computing, tele- and teamwork, and translation
tasks. The internal global consistency was adequate (Cronbach’s alpha in the pre-course questionnaire is 0.902 and the value for the
post-course questionnaire is 0.802).  Results show that collaborative work environments make the learning process easier, maintain students’
pre-existing positive disposition towards teamwork, and improve students’ self-confidence with regard to computers and translation tasks.
The data obtained from this study suggest that using a collaborative work platform in translation course is beneficial, enabling students to
gain confidence and feel satisfied with their work.
Study in cultural semantics of translation
Authors: Farhadiba Khan , Mohammed Mahameed
Published: July 2009

The aim of this paper is to consider the role of Cultural Semantics in Translation. This paper argues that it will never be a fair translation if something new has not been added to it. Therefore a degree of cultural interface between two language groups from (English to Indian language) is required for translating any text. Furthermore, this paper also gives an account of how in nineteenth century India the colonial agenda of translating indigenous texts was a part of a larger enterprise of Imperialism to the recent times where the attempt has been to rescue the work of translation from the restrictions imposed by the rhetoric of technical rules regarding transference from Source Language to Target Language. The result is one of complete fusion between the Source language and the Target Language.
Dialogical journal writing as ‘self‐therapy’: ‘I matter’
Authors: Wright Jeannie K.
Published: July 2009

Aim: This case study of one woman's (Jane's) experience of dialogical journal writing presents a way of finding a ‘compassionate image’ for self‐therapy. Various theoretical analyses are indicated with Mindfulness‐based conceptualisations at the forefront. Methodology: Based on three recorded interviews, the narrative inquiry took place over a year. Methodologically, this paper is also one contribution to an ongoing debate about different research approaches in therapeutic writing research. Participants: This study took place in Aotearoa New Zealand, where both Jane and I are migrants. Discussion: This account draws on a report of self‐directed writing for well‐being, seen as an alternative to counselling or medication for depression and anxiety. It focuses on how a particular style of writing evolved and how the motivation to write continues.
Prediction of protein β-residue contacts by Markov logic networks with grounding-specific weights
Authors: Lippi Marco , Frasconi Paolo
Published: July 2009

Motivation: Accurate prediction of contacts between β-strand residues can significantly contribute towards ab initio prediction of the 3D structure of many proteins. Contacts in the same protein are highly interdependent. Therefore, significant improvements can be expected by applying statistical relational learners that overcome the usual machine learning assumption that examples are independent and identically distributed. Furthermore, the dependencies among β-residue contacts are subject to strong regularities, many of which are known a priori. In this article, we take advantage of Markov logic, a statistical relational learning framework that is able to capture dependencies between contacts, and constrain the solution according to domain knowledge expressed by means of weighted rules in a logical language.

Results: We introduce a novel hybrid architecture based on neural and Markov logic networks with grounding-specific weights. On a non-redundant dataset, our method achieves 44.9% F1 measure, with 47.3% precision and 42.7% recall, which is significantly better (P < 0.01) than previously reported performance obtained by 2D recursive neural networks. Our approach also significantly improves the number of chains for which β-strands are nearly perfectly paired (36% of the chains are predicted with F1 ≥ 70% on coarse map). It also outperforms more general contact predictors on recent CASP 2008 targets.

Contact:  lippi@dsi.unifi.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
aGEM: an integrative system for analyzing spatial-temporal gene-expression information
Authors: Jiménez-Lozano Natalia , Segura Joan , Macías José Ramón , Vega Juanjo , Carazo José María
Published: July 2009

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers.

Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations.

Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http://agem.cnb.csic.es

Contact:  natalia@cnb.csic.es

Supplementary information:  Supplementary data are available at http://bioweb.cnb.csic.es/VisualOmics/aGEM/home.html and http://bioweb.cnb.csic.es/VisualOmics/index_VO.html and Bioinformatics online.
TileProbe: modeling tiling array probe effects using publicly available data
Authors: Judy Jennifer Toolan , Ji Hongkai
Published: July 2009

Motivation: Individual probes on an Affymetrix tiling array usually behave differently. Modeling and removing these probe effects are critical for detecting signals from the array data. Current data processing techniques either require control samples or use probe sequences to model probe-specific variability, such as with MAT. Although the MAT approach can be applied without control samples, residual probe effects continue to distort the true biological signals.

Results: We propose TileProbe, a new technique that builds upon the MAT algorithm by incorporating publicly available data sets to remove tiling array probe effects. By using a large number of these readily available arrays, TileProbe robustly models the residual probe effects that MAT model cannot explain. When applied to analyzing ChIP-chip data, TileProbe performs consistently better than MAT across a variety of analytical conditions. This shows that TileProbe resolves the issue of probe-specific effects more completely.

Availability:  http://www.biostat.jhsph.edu/∼hji/cisgenome/index_files/tileprobe.htm

Contact:  hji@jhsph.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
8‐Prenylkaempferol Suppresses Influenza A Virus‐Induced RANTES Production in A549 Cells via Blocking PI3K‐Mediated Transcriptional Activation of NF‐κB and IRF3
Authors: Chiou Wen-Fei , Chen Chen-Chih , Wei Bai-Luh
Published: July 2009

8‐Prenylkaempferol (8‐PK) is a prenylflavonoid isolated from Sophora flavescens, a Chinese herb with antiviral and anti‐inflammatory properties. In this study, we investigated its effect on regulated activation, normal T cell expressed and secreted (RANTES) secretion by influenza A virus (H1N1)‐infected A549 alveolar epithelial cells. Cell inoculation with H1N1 evoked a significant induction in RANTES accumulation accompanied with time‐related increase in nuclear translocation of nuclear factor‐κB (NF‐κB) and interferon regulatory factor 3 (IRF‐3), but showed no effect on c‐Jun phosphorylation. 8‐PK could significantly inhibit not only RANTES production but also NF‐κB and IRF‐3 nuclear translocation. We had proved that both NF‐κB and IRF‐3 participated in H1N1‐induced RANTES production since NF‐κB inhibitor pyrrolidinedithio carbamate (PDTC) and IRF‐3 siRNA attenuated significantly RANTES accumulation. H1N1 inoculation also increased PI3K activity as well as Akt phosphorylation and such responsiveness were attenuated by 8‐PK. In the presence of wortmannin, nuclear translocation of NF‐κB and IRF3 as well as RANTES production by H1N1 infection were all reversed, demonstrating that PI3K‐Akt pathway is essential for NF‐κB‐ and IRF‐3‐mediated RANTES production in A549 cells. Furthermore, 8‐PK but not wortmannin, prevented effectively H1N1‐evoked IκB degradation. In conclusion, 8‐PK might be an anti‐inflammatory agent for suppressing influenza A virus‐induced RANTES production acts by blocking PI3K‐mediated transcriptional activation of NF‐κB and IRF‐3 and in part by interfering with IκB degradation which subsequently decreases NF‐κB translocation.
North American (Panax quinquefolius) and Asian Ginseng (Panax ginseng) Preparations for Prevention of the Common Cold in Healthy Adults: A Systematic Review
Authors: Seida Jennifer Krebs , Durec Tamara , Kuhle Stefan
Published: July 2009

Background: Standardized ginseng extract has become the best‐selling cold and flu remedy in Canada, yet much controversy regarding the efficacy of ginseng in preventing common colds remains. Objective: To assess the efficacy of ginseng preparations for the prevention of common colds in healthy adults. Methods: Comprehensive bibliographic database, trial registry and grey literature searches were conducted up to December 2007. Randomized controlled trials or controlled clinical trials comparing North American (Panax quinquefolius) or Asian ginseng (Panax ginseng) root extract to placebo or no treatment in healthy adults were included. Two reviewers independently applied the study selection criteria and assessed methodological quality. Results: Five trials involving 747 participants were included. All five trials examined North American ginseng. The methodological quality of the trials varied widely. Ginseng preparations significantly reduced the total number of common colds by 25% compared to placebo (one trial; 95% CI: 5–45). There was a tendency toward a lower incidence of having at least one common cold or other acute respiratory infection (ARI) in the ginseng group compared to the placebo group (five trials; relative risk: 0.70; 95% CI: 0.48–1.02). Compared to placebo, ginseng significantly shortened the duration of colds or ARIs by 6.2 days (two trials; 95% CI: 3.4–9.0). Conclusions: There is insufficient evidence to conclude that ginseng reduces the incidence or severity of common colds. North American ginseng appears to be effective in shortening the duration of colds or ARIs in healthy adults when taken preventatively for durations of 8–16 weeks.
Ethanol Extract of Fructus Schisandrae Decreases Hepatic Triglyceride Level in Mice Fed with a High Fat/Cholesterol Diet, with Attention to Acute Toxicity
Authors: Pan Si-Yuan , Yu Zhi-Ling , Dong Hang , Xiang Chun-Jing , Fong Wang-Fun , Ko Kam-Ming
Published: July 2009

Effects of the ethanol extract of Fructus Schisandrae (EtFSC) on serum and liver lipid contents were investigated in mice fed with high fat/cholesterol (HFC) diet for 8 or 15 days. The induction of hypercholesterolemia by HFC diet caused significant increases in serum and hepatic total cholesterol (TC) levels (up to 62% and 165%, resp.) and hepatic triglyceride (TG) levels (up to 528%) in mice. EtFSC treatment (1 or 5 g/kg/day for 7 days; from Day 1 to 7 or from Day 8 to 14, i.g.) significantly decreased the hepatic TG level (down to 35%) and slightly increased the hepatic index (by 8%) in hypercholesterolemic mice. Whereas fenofibrate treatment (0.1 g/kg/day for 7 days, i.g.) significantly lowered the hepatic TG level (by 61%), it elevated the hepatic index (by 77%) in hypercholesterolemic mice. Acute toxicity test showed that EtFSC was relatively non‐toxic, with an LD50 value of 35.63 ± 6.46 g/kg in mice. The results indicate that EtFSC treatment can invariably decrease hepatic TG in hypercholesterolemic mice, as assessed by both preventive and therapeutic protocols, suggesting its potential use for fatty liver treatment.
Investigation of Electroacupuncture and Manual Acupuncture on Carnitine and Glutathione in Muscle
Authors: Toda Shizuo
Published: July 2009

Electroacupuncture (EA) and manual acupuncture (MA) have therapeutic effects on muscle fatigue in muscle disease. The deficiencies of carnitine and glutathione induce muscle fatigue. This report investigated the effects of EA and MA on carnitine and glutathione in muscle. After the mice of EA group were fixed in the animal cage, right Zusanli (ST36) and Jiexi (ST41) were acupunctured and stimulated with uniform reinforcing and reducing method by twirling the acupuncture needle for 15 min. And then, the needle handles were connected to an electric stimulator for stimulating the acupoint with dense‐sparse waves. After the mice of MA group were fixed in an animal cage, right ST36 and ST41 were acupunctured and allowed for 15 min. The mice of normal control group were not acupunctured and stimulated for 15 min. The mice of all groups were killed for collecting muscle tissue 1 h after the final treatment. Carnitine and glutathione in homogenate of muscle tissue were determined with carnitine (Kainos Laboratories Co., Tokyo, Japan) and glutathione assay kit (Dojin Chemicals Co., Kumamoto, Japan). Carnitine level in muscle tissue of MA group was significantly higher than those of EA group and normal control group. Carnitine level in muscle tissue of EA group was not significantly different from that of normal control group. Glutathione levels in muscle tissue of EA group and MA group were significantly higher than that of normal control group. This report presented that carnitine in muscle is increased by MA, and not increased by EA, and that glutathione in muscle is increased by EA and MA.
Intestinal Anti‐Inflammatory Activity ofBaccharis dracunculifoliain the Trinitrobenzenesulphonic Acid Model of Rat Colitis
Authors: Cestari Sílvia Helena , Bastos Jairo Kennup , Di Stasi Luiz Claudio
Published: July 2009

Baccharis dracunculifoliaDC (Asteraceae) is a Brazilian medicinal plant popularly used for its antiulcer and anti‐inflammatory properties. This plant is the main botanical source of Brazilian green propolis, a natural product incorporated into food and beverages to improve health. The present study aimed to investigate the chemical profile and intestinal anti‐inflammatory activity ofB. dracunculifoliaextract on experimental ulcerative colitis induced by trinitrobenzenosulfonic acid (TNBS). Colonic damage was evaluated macroscopically and biochemically through its evaluation of glutathione content and its myeloperoxidase (MPO) and alkaline phosphatase activities. Additionalin vitroexperiments were performed in order to test the antioxidant activity by inhibition of induced lipid peroxidation in the rat brain membrane. Phytochemical analysis was performed by HPLC using authentic standards. The administration of plant extract (5 and 50 mg kg−1) significantly attenuated the colonic damage induced by TNBS as evidenced both macroscopically and biochemically. This beneficial effect can be associated with an improvement in the colonic oxidative status, since plant extract prevented glutathione depletion, inhibited lipid peroxidation and reduced MPO activity. Caffeic acid,p‐coumaric acid, aromadendrin‐4‐O‐methyl ether, 3‐prenyl‐p‐coumaric acid, 3,5‐diprenyl‐p‐coumaric acid and baccharin were detected in the plant extract.
Bufalin Induces Reactive Oxygen Species Dependent Bax Translocation and Apoptosis in ASTC‐a‐1 Cells
Authors: Sun Lei , Chen Tongsheng , Wang Xiaoping , Chen Yun , Wei Xunbin
Published: July 2009

Bufalin has been shown to induce cancer cell death through apoptotic pathways. However, the molecular mechanisms are not well understood. In this study, we used the confocal fluorescence microscopy (CFM) to monitor the spatio‐temporal dynamics of reactive oxygen species (ROS) production, Bax translocation and caspase‐3 activation during bufalin‐induced apoptosis in living human lung adenocarcinoma (ASTC‐a‐1) cells. Bufalin induced ROS production and apoptotic cell death, demonstrated by Hoechst 33258 staining as well as flow cytometry analysis. Bax redistributed from cytosol to mitochondria from 12 to 48 h after bufalin treatment in living cells expressed with green fluorescent protein Bax. Treatment with the antioxidant N‐acetyl‐cysteine (NAC), a ROS scavenger, inhibited ROS generation and Bax translocation and led to a significant protection against bufalin‐induced apoptosis. Our results also revealed that bufalin induced a prominent increase of caspase‐3 activation blocked potently by NAC. Taken together, bufalin induced ROS‐mediated Bax translocation, mitochondrial permeability transition and caspase‐3 activation, implying that bufalin induced apoptosis via ROS‐dependent mitochondrial death pathway in ASTC‐a‐1 cells.
The Birth of the North American Home Improvement Store, 1905–1929
Authors: Harris Richard
Published: July 2009

The idea, and to a lesser extent the reality, of themodern home improvement store was born in the first quarter of the twentieth century. After 1905 the manufacturers of mail-order kit houses soon grew to threaten the local monopoly of retail building suppliers. Themost important of these suppliers were the lumber merchants who provided most of the materials and credit used by building contractors. At first dealers responded by mounting boycotts and by supporting trade-at-home campaigns, but these were successfully challenged in court. A survey of trade journals shows that after 1914 dealers began to act more constructively. Encouraged by the trade press, and helped by state and national associations, by the 1920s they were advertising more effectively and offering a widening range of goods and services to consumers, including house plans. Because many new customers were women, dealers had to hire more courteous staff, clean up their yards, mount better displays, build showrooms and, in time, relocate to more salubrious and heavily-trafficked parts of town. The emergence of the home improvement store is a significant chapter in the history of urban housing, and especially the marketing of housing services, in the twentieth century.
The impact of commercial fishing on the determination of habitat associations for sea scallops (Placopecten magellanicus, Gmelin)
Authors: Smith Stephen J. , Black Jerry , Todd Brian J. , Kostylev Vladimir E. , Lundy Mark J.
Published: July 2009

Smith, S. J., Black, J., Todd, B. J., Kostylev, V. E. and Lundy, M. J. 2009. The impact of commercial fishing on the determination of habitat associations for sea scallops (Placopecten magellanicus, Gmelin). – ICES Journal of Marine Science, 66: 2043–2051. The sea scallop (Placopecten magellanicus) population off southwestern Nova Scotia in Scallop Fishing Area 29 has been monitored by an annual drag survey since the fishery started there in 2001. A new stratification scheme based on surficial geology maps from a multibeam bottom mapping and geology ground-truth project completed in 2004 in the area have been used for survey design since 2005. Survey data from before 2005 have been post-stratified using the new strata. The efficiency of the design with respect to variance reduction appears to have diminished over time suggesting that the association between scallop abundance and bottom type may not have been as strong or constant as first assumed. Modelling of the association between scallop abundance and bottom type and depth using a Bayesian hierarchical approach confirms this diminishing relationship. Comparison of the results from the model with spatial measures of fishing effort based on satellite vessel monitoring data suggests that increasing exploitation may be masking the relationships as scallop beds are targeted and fished down. These results could have implications on the interpretation of species habitat associations from areas where data are only available from periods when the populations have been exploited over a long time. In these cases, the spatial distribution of fishing effort may be a better indicator of species habitat associations than the estimates from surveys.
CCR1 expression and signal transduction by murine BMMC results in secretion of TNF-α, TGFβ-1 and IL-6
Authors: Fifadara Nimita H. , Aye Cho Cho , Raghuwanshi Sandeep K. , Richardson Ricardo M. , Ono Santa Jeremy
Published: July 2009

Chemokine receptors (CCRs) are important co-stimulatory molecules found on many blood cells and associated with various diseases. The expression and function of CCRs on mast cells has been quite controversial. In this study, we report for the first time that murine bone marrow-derived mast cells (BMMC) express messenger RNA and protein for CCR1. BMMC cultured in the presence of murine recombinant stem cell factor and murine IL-3 expressed CCR1 after 5–6 weeks. We also report for the first time that mBMMCCCR1+ cells endogenously express neurokinin receptor-1 and intercellular adhesion molecule-1. To examine the activity of CCR1 on these BMMC, we simultaneously stimulated two receptors: CCR1 by its ligand macrophage inflammatory protein-1α and the IgE receptor FcεRI by antigen cross-linking. We found that co-stimulation enhanced BMMC degranulation compared with FcεRI stimulation alone, as assessed by β-hexosaminidase activity (85 versus 54%, P < 0.0001) and Ca2+ influx (223 versus 183 nM, P < 0.05). We also observed significant increases in mast cell secretion of key growth factors, cytokines and chemokine mediators upon CCR1–FcεRI co-stimulation. These factors include transforming growth factor β-1, tumor necrosis factor-α and the cytokine IL-6. Taken together, our data indicate that CCR1 plays a key role in BMMC function. These findings contribute to our understanding of mechanisms for immune cell trafficking during inflammation.
High-resolution mapping and analysis of copy number variations in the human genome: A data resource for clinical and research applications
Authors: Shaikh Tamim H. , Gai Xiaowu , Perin Juan C. , Glessner Joseph T. , Xie Hongbo , Murphy Kevin , O'Hara Ryan , Casalunovo Tracy , Conlin Laura K. , D'Arcy Monica , Frackelton Edward C. , Geiger Elizabeth A. , Haldeman-Englert Chad , Imielinski Marcin , Kim Cecilia E. , Medne Livija , Annaiah Kiran , Bradfield Jonathan P. , Dabaghyan Elvira , Eckert Andrew , Onyiah Chioma C. , Ostapenko Svetlana , Otieno F. George , Santa Erin , Shaner Julie L. , Skraban Robert , Smith Ryan M. , Elia Josephine , Goldmuntz Elizabeth , Spinner Nancy B. , Zackai Elaine H. , Chiavacci Rosetta M. , Grundmeier Robert , Rappaport Eric F. , Grant Struan F.A. , White Peter S. , Hakonarson Hakon
Published: July 2009

We present a database of copy number variations (CNVs) detected in 2026 disease-free individuals, using high-density, SNP-based oligonucleotide microarrays. This large cohort, comprised mainly of Caucasians (65.2%) and African-Americans (34.2%), was analyzed for CNVs in a single study using a uniform array platform and computational process. We have catalogued and characterized 54,462 individual CNVs, 77.8% of which were identified in multiple unrelated individuals. These nonunique CNVs mapped to 3272 distinct regions of genomic variation spanning 5.9% of the genome; 51.5% of these were previously unreported, and >85% are rare. Our annotation and analysis confirmed and extended previously reported correlations between CNVs and several genomic features such as repetitive DNA elements, segmental duplications, and genes. We demonstrate the utility of this data set in distinguishing CNVs with pathologic significance from normal variants. Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics.
RazerS—fast read mapping with sensitivity control
Authors: Weese David , Emde Anne-Katrin , Rausch Tobias , Döring Andreas , Reinert Knut
Published: July 2009

Second-generation sequencing technologies deliver DNA sequence data at unprecedented high throughput. Common to most biological applications is a mapping of the reads to an almost identical or highly similar reference genome. Due to the large amounts of data, efficient algorithms and implementations are crucial for this task. We present an efficient read mapping tool called RazerS. It allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. Our tool can work either lossless or with a user-defined loss rate at higher speeds. Given the loss rate, we present an approach that guarantees not to lose more reads than specified. This enables the user to adapt to the problem at hand and provides a seamless tradeoff between sensitivity and running time.
Unusual composition of a yeast chromosome arm is associated with its delayed replication
Authors: Payen Célia , Fischer Gilles , Marck Christian , Proux Caroline , Sherman David James , Coppée Jean-Yves , Johnston Mark , Dujon Bernard , Neuvéglise Cécile
Published: July 2009

The 11.3-Mb genome of the yeast Lachancea (Saccharomyces) kluyveri displays an intriguing compositional heterogeneity: a region of ∼1 Mb, covering almost the whole left arm of chromosome C (C-left), has an average GC content of 52.9%, which is significantly higher than the 40.4% global GC content of the rest of the genome. This region contains the MAT locus, which remains normal in composition. The excess of GC base pairs affects both coding and noncoding sequences, and thus is not due to selective pressure acting on protein sequences. It leads to a strong codon usage bias and alters the amino acid composition of the 457 proteins encoded on C-left that do not show obvious bias for functional categories, or the presence of paralogs or orthologs of essential genes of Saccharomyces cerevisiae. They share significant synteny conservation with other species of the Saccharomycetaceae, and phylogenetic analysis indicates that C-left originates from a Lachancea species. In contrast, there is a complete absence of transposable elements in C-left, whereas 18 elements per megabase are distributed across the rest of the genome. Comparative hybridization of synchronized cells using high-density genome arrays reveals that C-left is replicated later during S phase than the rest of the genome. Two possible primary causes of this major compositional heterogeneity are discussed: an ancient hybridization of two related species with very distinct GC composition, or an intrinsic mechanism, possibly associated with the loss of the silent cassettes from C-left that progressively increased the GC content and generated the delayed replication of this chromosomal arm.
Computational Identification of Potential Molecular Interactions in Arabidopsis
Authors: Lin Mingzhi , Hu Bin , Chen Lijuan , Sun Peng , Fan Yi , Wu Ping , Chen Xin
Published: July 2009

Knowledge of the protein interaction network is useful to assist molecular mechanism studies. Several major repositories have been established to collect and organize reported protein interactions. Many interactions have been reported in several model organisms, yet a very limited number of plant interactions can thus far be found in these major databases. Computational identification of potential plant interactions, therefore, is desired to facilitate relevant research. In this work, we constructed a support vector machine model to predict potential Arabidopsis (Arabidopsis thaliana) protein interactions based on a variety of indirect evidence. In a 100-iteration bootstrap evaluation, the confidence of our predicted interactions was estimated to be 48.67%, and these interactions were expected to cover 29.02% of the entire interactome. The sensitivity of our model was validated with an independent evaluation data set consisting of newly reported interactions that did not overlap with the examples used in model training and testing. Results showed that our model successfully recognized 28.91% of the new interactions, similar to its expected sensitivity (29.02%). Applying this model to all possible Arabidopsis protein pairs resulted in 224,206 potential interactions, which is the largest and most accurate set of predicted Arabidopsis interactions at present. In order to facilitate the use of our results, we present the Predicted Arabidopsis Interactome Resource, with detailed annotations and more specific per interaction confidence measurements. This database and related documents are freely accessible at http://www.cls.zju.edu.cn/pair/.
The personal curation of digital objects
Authors: Williams Peter , Leighton John Jeremy , Rowland Ian
Published: July 2009

Purpose

This paper aims to set out a coherent intellectual framework to help to better understand how people create, organise, manage, use and dispose of their personal digital archives. The context for this is the increasing volume and diversity of digital information objects being captured and stored by individuals in their personal capacities and the need to find ways to preserve this material for posterity.

Design/methodology/approach

The research presented here is based on literature analysis, the questions having been informed by an earlier series of in‐depth interviews. The approach taken is to synthesise key concepts from the computer science, information management, and archives and records management literatures. Key concepts from the existing literature in computer science, information management, and archives and records management were elicited and synthesised to create a coherent document lifecycle narrative.

Findings

Individuals exhibit great diversity in terms of personal information management and digital archiving practice at just about every point in the digital information cycle: much more so than is the case in formal repositories. Practices exhibited are not always conducive to efficient document management. This represents a very keen challenge for professional curatorial practice.

Practical implications

Little is known about how individuals manage digital information resources in their personal capacity, outside of their corporate or institutional employment. Yet both individuals on their own and professional curators on behalf of repositories are increasingly being faced with the challenge of how to deal with digital media. It is hoped that this paper will contribute to a growing debate in this area.

Originality/value

Personal information management from the perspective of personal digital archives is a surprisingly under‐researched area and the proposed model adopts an archival information lifecycle approach. It seeks to apply and promote an archivally‐oriented personal information management.
The digital native – myth and reality
Authors: Selwyn Neil
Published: July 2009

Purpose

The purpose of this paper is to develop and promote a realistic understanding of young people and digital technology with a view to supporting information professionals in playing useful and meaningful roles in supporting current generations of young people. In particular the paper aims to offer a critical perspective on popular and political understandings of young people and digital technologies – characterised by notions of “digital natives”, the “net generation” and other commonsense portrayals of expert young technology users. The paper seeks to consider the accuracy of such descriptions in reflecting young people's actual uses of digital technology and digital information.

Design/methodology/approach

The paper provides a comprehensive review of the recent published literatures on young people and digital technology in information sciences, education studies and media/communication studies.

Findings

The findings show that young people's engagements with digital technologies are varied and often unspectacular – in stark contrast to popular portrayals of the digital native. As such, the paper highlights a misplaced technological and biological determinism that underpins current portrayals of children, young people and digital technology.

Originality/value

The paper challenges the popular assumption that current generations of children and young people are innate, talented users of digital technologies. Having presented a more realistic basis for approaching generational differences in technology use, the paper explores the functions and roles that information professionals can be expected to play in supporting young people in the digital age.