bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extrapulmonary Dissemination of
Mycobacterium bovis
but Not
Mycobacterium tuberculosis
in a Bronchoscopic Rabbit Model of Cavitary Tuberculosis
Authors: Nedeltchev Gueno G. , Raghunand Tirumalai R. , Jassal Mandeep S. , Lun Shichun , Cheng Qi-Jian , Bishai William R. 
Published: December 2008

ABSTRACT

The rabbit model of tuberculosis is attractive because of its pathophysiologic resemblance to the disease in humans. Rabbits are naturally resistant to infection but may manifest cavitary lung lesions. We describe here a novel approach that utilizes presensitization and bronchoscopic inoculation to reliably produce cavities in the rabbit model. With a fixed inoculum of bacilli, we were able to reproducibly generate cavities by using
Mycobacterium bovis
Ravenel,
M. bovis
AF2122,
M. bovis
BCG,
M. tuberculosis
H37Rv,
M. tuberculosis
CDC1551, and the
M. tuberculosis
CDC1551 Δ
sig
C mutant.
M. bovis
infections generated cavitary CFU counts of 10
6
to 10
9
bacilli, while non-
M. bovis
species and BCG yielded CFU counts that ranged from 10
4
to 10
8
bacilli. Extrapulmonary dissemination was almost exclusively noted among rabbits infected with
M. bovis
Ravenel and AF2122. Though all of the species yielded secondary lesions at intrapulmonary sites,
M. bovis
infections led to the most apparent gross pathology. Using the
M. tuberculosis icl
and
dosR
gene expression patterns as molecular sentinels, we demonstrated that both the cavity wall and cavity lumen are microenvironments associated with hypoxia, upregulation of the bacterial dormancy program, and the use of host lipids for bacterial catabolism. This unique cavitary model provides a reliable animal model to study cavity pathogenesis and extrapulmonary dissemination.
Cytogeography of Solidago subsect. Glomeruliflorae (Asteraceae: Astereae)
Authors: Cook Rachel E. , Semple John C. 
Published: December 2008

Chromosome numbers were determined for 347 individuals of Solidago subsect. Glomeruliflorae (Torr. & A. Gray) Nesom, including 151 new reports. Previously unpublished documented reports are for the following taxa: Solidago caesia L. var. caesia R.E. Cook & Semple, S. caesia var. zedia R.E. Cook & Semple, Solidago curtisii Torr. & A. Gray var. curtisii (Small) R.E. Cook & Semple, S. curtisii var. flaccidifolia (Small) R.E. Cook & Semple, Solidago flexicaulis L., Solidago glomerata Michx., and Solidago lancifolia (Torr. & A. Gray) Chapm. All counts for S. caesia, Solidago macrophylla Pursh., and Solidago ouachitensis Taylor & Taylor were diploid (2n = 18). Two published counts for Solidago albopilosa E.L. Braun were tetraploid. Counts of 2n = 18 and 36 were made for S. flexicaulis. Counts of 2n = 18, 36, and 54 were made for S. curtisii. Counts of 2n = 108 and 126 were made for S. glomerata, and 2n = 90 for S. lancifolia. Cytogeographic maps of S. albopilosa , S. caesia var. caesia, S. curtisii var. curtisii, S. curtisii var. flaccidifolia, S. flexicaulis, S. glomerata, S. lancifolia, S. macrophylla, and S. ouachitensis were prepared including all counts. The following are first documented reports for the taxon: S. caesia var. zedia , 2n = 18, one population; S. lancifolia, 2n = 90, four populations.
The rotated-lamina syndrome. VIII. Lamina rotation and anisophylly in two species ofElatostema(Urticacae), and early development of seedlings ofE. sessile
Authors: Charlton W. A. 
Published: December 2008

Elatostema rugosum A. Cunn. and Elatostema sessile J.R. Forst. & G. Forst. have dorsiventral shoots in which the leaves are arranged in anisophyllous pairs forming four ranks: two on the dorsal and two on the ventral side of the shoot. The ventral leaves have expanded asymmetrical leaf blades with lamina rotation, i.e., the lamina develops in the bud facing towards the upper side of the shoot rather than towards the shoot apex. Each ventral leaf has an asymmetrical intrapetiolar stipule. Lamina rotation occurs by asymmetrical development at the base of the leaf blade above the attachment of the stipule. The dorsal leaves are small, scale-like, approximately symmetrical exstipulate structures. The development of the ventral leaf is generally similar to that found in previous studies of related anisophyllous cases, but the dorsal leaf is reduced to a scale and is simpler than in related cases. Seedlings of E. sessile have been examined to investigate the way in which the combination of unusual features of shoot structure is produced, and also to cast light on the homology of the dorsal leaf. Anisophylly and asymmetry appear in the first pair of leaves formed above the cotyledons in seedlings and become accentuated in subsequent pairs. Events in seedlings suggest the dorsal leaf is derived by reduction from an initial state with blade, stipule, and basal region to the basal region alone. The rapid establishment of lamina rotation and asymmetry in the seedling shoot differs from most other cases described and adds to previous arguments that lamina rotation has arisen independently in a number of taxonomic groups.
Jessie's Dream at Lucknow
Authors: Mukharji Projit Bihari 
Published: December 2008

Nineteenth-century British histories of the Indian ‘Mutiny’ have usually been seen as a moment of unequivocal imperial confidence. Little account has been taken of the large number of complex, non-historical texts that memorialized the ‘Mutiny’. Victorian Britain witnessed a wide and varied interest in the representation of events of the past. The representations spanned many genres and continually multiplied in form and medium under the impetus of an expanding commodity culture. Commoditized memorial texts—unlike professional histories—are read by an extremely diverse group of people. The wide dissemination and variety made the texts semantically unstable. By concentrating on non-historical memorial texts of the ‘Mutiny’ and by attending to both their production and consumption, we can discern a far wider set of attitudes towards the ‘Mutiny’. Not only are many of these texts revealed to be ambivalent towards the imperial project, but also indeed they reveal a multiplicity of fissures within Victorian society.
Mining for gold in the blogosphere
Authors: Dale Iain 
Published: December 2008

Top bloggers have become more influential than many print journalism specialists. But how many make the web pay? In the United States political bloggers have taken on an importance that would be unthinkable in the UK, writes top UK political blogger Dale. In Britain it’s very different. The development of the UK political blogosphere, while much heralded in almost weekly newspaper features, is way behind that of the United States. Few bloggers have any sort of media profile and even fewer make any money at all out of their online activities… Blogs here haven’t got the moneymaking ability of those in the US, or their influence, or their profile. But in three or four years, they just might.
Labour's love lost?
Authors: Seddon Mark 
Published: December 2008

Once again the left-wing Tribune's future is uncertain. Why is it, asks a former editor, that publications of the Left often fail to thrive? A former editor of Tribune observes that the left-wing publication’s future is once again under threat and asks to what extent is the permanently cash-strapped years of Tribune’s existence and its possible closure a measure of a decline amongst the political weeklies. “There is an uncomfortable truth for the Left, and this at a time when the future for the niche market weeklies looks a good deal more promising than it does for many daily newspapers. It is that for the last 30 years, magazines of the Right, such as The Spectator, have tended to prosper, while New Statesman and Tribune, and on the Communist left, the daily Morning Star, have slowly declined.”
How SEO is changing journalism
Authors: Richmond Shane 
Published: December 2008

Search engine optimisation can ensure content attracts maximum web hits. And it doesn't mean conning readers, says an online editor The communities editor of Telegraph.co.uk advocates the writing of articles and headlines with search criteria as a guide. But search engines will not end up dictating our news agenda as well as the way we format our stories, he argues: “Giving readers what they want is a sensible strategy, even though the overall mix of stories within a publication has to be balanced. Different editors will make different choices, but they are editorial choices, not SEO choices. SEO is value neutral. It doesn’t require you to dumb down, to fill your stories with the names of celebrities or to write 500 articles about Viagra every month. Even if you write about badgers, thermal dynamics or parachuting you will want your article to be seen by people who care about those topics. SEO techniques will give your article a better chance of being found.”
Holding ourselves accountable
Authors: Pritchard Stephen 
Published: December 2008

U.S. papers dispensing with their ombudsmen are misguided, it is argued. Transparency is vital to rebuild public trust The ombudsman of The Observer newspaper notes that editors of American newspapers are shedding staff at an alarming rate as the financial crisis translates into a sharp downturn in advertising and readerships melt away and that among the casualties are 12 news ombudsmen: men and women who work within newsrooms, dealing with complaints, publishing corrections and writing columns and internal memos on their papers’ journalism. He believes that this short-term thinking is wrong and those in the UK who have yet to appoint an ombudsman need to ask themselves if they can afford to be without one: “It’s all about transparency. From transparency flows trust. Show your readers that you care about accuracy, about fairness, about getting the story right and you gain their trust. If they trust you they will buy you.”
Different horses, different courses
Authors: Delano Anthony 
Published: December 2008

Media degrees have been under attack, even in this journal. An educator defends the values of higher journalistic education Journalists turned academic Delano writes that few occupations display such a gulf between ideals and reality as journalism and journalism education is no different. Journalism graduates will learn whatever their particular university is best able to offer. Universities are far from equal. Some turn out better history or science graduates than others. Some have demanding entrance requirements; others are so desperate for funding that they will admit virtually all comers. Some will not have the equipment to teach journalism to modern requirements; administration or staff may not be up to the job… So what is the value of a journalism degree? Even though it is now being taught and studied as never before, journalism continues to elude definition.
Participatory approaches to promote healthy lifestyles among Turkish and Moroccan women in Amsterdam
Authors: Wagemakers Annemarie , Corstjens Renée , Koelen Maria , Vaandrager Lenneke , van't Riet Hilda , Dijkshoorn Henriëtte 
Published: December 2008

Although it is recognized that community health promotion succeeds or fails by level of participation, effectiveness and benefits of community programs are underestimated, because participation is seldom monitored and evaluated. In the Dutch “Healthy Lifestyle Westerpark” program in Amsterdam, participation was both the main working principle and the main goal. Between 2003 and 2006, the Municipal Health Service (MHS) carried out a qualitative study on the background of overweight in Turkish and Moroccan women aged 25 to 45 years and on possibilities for promoting health with and for the target group. The aim of the program was to increase the women's participation and to evaluate participation levels in all phases. The research aim of this paper is to contribute to the development of participatory methods. Needs assessment and intervention development phases resulted in implementation of aerobic lessons and nutrition interventions. In the evaluation phase, participation levels were measured using Pretty's typology in focus groups. Results show that women appreciate participating in the program. Increase in physical activity was not measured. Women's knowledge about healthy food increased, women changed behavior by buying healthier food ingredients and women continued to participate. Participatory approaches facilitate participation at the desired level in the different phases of the program. Participatory approaches are time-consuming but worthwhile. Pretty's typology is useful to measure degree of participation, although methods can be improved and the meaning of participation should be reconsidered. The added value of this article is twofold: 1. it demonstrates that participatory methods and tools both facilitate and evaluate participation, and 2. it shows how to evaluate the degree of participation. (Promot Educ, 2008; 15 (4): pp. 17-23)
Provision of essential obstetric care (EOC): a sine qua non to reducing maternal mortality rate in Nigeria
Authors: Ibekwe Perpetus C. , Ibekwe Rosemary O. 
Published: December 2008

Nigeria's maternal mortality rate has been on the increase even after the launching of the Safe Motherhood Initiative (SMI) 16 years ago. The causes of this increase are well known, and mainly result from inability of a health system to deal effectively with complications, especially during or shortly after childbirth. Shortage of health professionals and health facilities equipped to offer EOC and emergency obstetric care 24 hours a day are significantly related to quality of care and maternal mortality rates. Since the Primary Health Care (PHC) level is usually the first contact point for the majority of our women, it must be able to deliver the essential services in full and make appropriate referrals when necessary. From available statistics, provision of EOC services in Nigeria has been deplorable. Deficient areas within the health system concerning EOC services are highlighted and suggestions made on how to improve and sustain services. It is concluded that provision of effective and efficient EOC facilities and services will play a key role in maternal mortality reduction, not only in Nigeria but in most developing regions of the world. (Promot Educ, 2008; 15 (4): pp. 50-52)
Beyond SARS: ethnic community organization's role in public health — a Toronto experience
Authors: Weizhen Dong  
Published: December 2008

The SARS outbreak in Toronto was a public health crisis. It was particularly frightening to the Chinese-Canadians, because of the origin of the deadly disease. The Chinese-Canadian community organizations launched various activities to help the Chinese-Canadians as well as other Asian-Canadian communities to fight against SARS and its social side-effects. From launching the SARS Supporting Line, distributing health promotional material, disseminating SARS related information, paying tribute to frontline health workers, and promoting local business, to fundraising for SARS related research; they played an active role in easing the public's anxiety, especially for the Chinese-Canadians in the great Toronto area. The culturally diverse population brought problems as well as solutions. Ethnic groups have expertise in almost all areas, including people with leadership skills. The Toronto Chinese community's experience in combating SARS is a good example. The Chinese-Canadian community organizations' activities during the SARS outbreak demonstrate that ethnic minority organizations can play an important role in public health, especially in a public health crisis, and beyond. (Promot Educ, 2008; 15 (4): pp. 53-55)
Nonmyeloablative allografting for newly diagnosed multiple myeloma: the experience of the Gruppo Italiano Trapianti di Midollo
Authors: Bruno Benedetto , Rotta Marcello , Patriarca Francesca , Mattei Daniele , Allione Bernardino , Carnevale-Schianca Fabrizio , Sorasio Roberto , Rambaldi Alessandro , Casini Marco , Parma Matteo , Bavaro Pasqua , Onida Francesco , Busca Alessandro , Castagna Luca , Benedetti Edoardo , Iori Anna Paola , Giaccone Luisa , Palumbo Antonio , Corradini Paolo , Fanin Renato , Maloney David , Storb Rainer , Baldi Ileana , Ricardi Umberto , Boccadoro Mario 
Published: December 2008

AbstractDespite recent advances, allografting remains the only potential cure for myeloma. From July 1999 to June 2005, 100 newly diagnosed patients younger than 65 years were enrolled in a prospective multicenter study. First-line treatment included vincristin, adriamycin, and dexamethasone (VAD)–based induction chemotherapy, a cytoreductive autograft (melphalan 200 mg/m2) followed by a single dose of nonmyeloablative total body irradiation and allografting from an human leukocyte antigen (HLA)–identical sibling. Primary end points were the overall survival (OS) and event-free survival (EFS) from diagnosis. After a median follow-up of 5 years, OS was not reached, and EFS was 37 months. Incidences of acute and chronic graft-versus-host disease (GVHD) were 38% and 50%, respectively. Complete remission (CR) was achieved in 53% of patients. Profound cytoreduction (CR or very good partial remission) before allografting was associated with achievement of posttransplantation CR (hazard ratio [HR] 2.20, P = .03) and longer EFS (HR 0.33, P < .01). Conversely, development of chronic GVHD was not correlated with CR or response duration. This tandem transplantation approach allows prolonged survival and long-term disease control in patients with reduced tumor burden at the time of allografting. We are currently investigating the role of “new drugs” in intensifying pretransplantation cytoreduction and posttransplantation graft-versus-myeloma effects to further improve clinical outcomes. (http://ClinicalTrials.gov; NCT-00702247.)
LAD-1/variant syndrome is caused by mutations in FERMT3
Authors: Kuijpers Taco W. , van de Vijver Edith , Weterman Marian A. J. , de Boer Martin , Tool Anton T. J. , van den Berg Timo K. , Moser Markus , Jakobs Marja E. , Seeger Karl , Sanal Özden , Ünal Sule , Çetin Mualla , Roos Dirk , Verhoeven Arthur J. , Baas Frank 
Published: December 2008

AbstractLeukocyte adhesion deficiency-1/variant (LAD1v) syndrome presents early in life and manifests by infections without pus formation in the presence of a leukocytosis combined with a Glanzmann-type bleeding disorder, resulting from a hematopoietic defect in integrin activation. In 7 consanguineous families, we previously established that this defect was not the result of defective Rap1 activation, as proposed by other investigators. In search of the genetic defect, we carried out homozygosity mapping in 3 of these patients, and a 13-Mb region on chromosome 11 was identified. All 7 LAD1v families share the same haplotype, in which 3 disease-associated sequence variants were identified: a putative splice site mutation in CALDAGGEF1 (encoding an exchange factor for Rap1), an intronic 1.8-kb deletion in NRXN2, and a premature stop codon (p.Arg509X) in FERMT3. Two other LAD1v patients were found to carry different stop codons in FERMT3 (p.Arg573X and p.Trp229X) and lacked the CALDAGGEF1 and NRXN2 mutations, providing convincing evidence that FERMT3 is the gene responsible for LAD1v. FERMT3 encodes kindlin-3 in hematopoietic cells, a protein present together with integrins in focal adhesions. Kindlin-3 protein expression was undetectable in the leukocytes and platelets of all patients tested. These results indicate that the LAD1v syndrome is caused by truncating mutations in FERMT3.
IDEA: Interactive Display for Evolutionary Analyses
Authors: Simons Rain , Mahurkar Anup , Crabtree Jonathan , Badger Jonathan H , Carlton Jane M , Silva Joana C 
Published: December 2008

Abstract
Background
The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of interest an increasingly important approach to addressing broad evolutionary questions. Two of the programs most widely used for this purpose are codeml and baseml, parts of the PAML (Phylogenetic Analysis by Maximum Likelihood) suite. A significant drawback of these programs is their lack of a graphical user interface, which can limit their user base and considerably reduce their efficiency.

Results
We have developed IDEA (Interactive Display for Evolutionary Analyses), an intuitive graphical input and output interface which interacts with PHYLIP for phylogeny reconstruction and with codeml and baseml for molecular evolution analyses. IDEA's graphical input and visualization interfaces eliminate the need to edit and parse text input and output files, reducing the likelihood of errors and improving processing time. Further, its interactive output display gives the user immediate access to results. Finally, IDEA can process data in parallel on a local machine or computing grid, allowing genome-wide analyses to be completed quickly.

Conclusion
IDEA provides a graphical user interface that allows the user to follow a codeml or baseml analysis from parameter input through to the exploration of results. Novel options streamline the analysis process, and post-analysis visualization of phylogenies, evolutionary rates and selective constraint along protein sequences simplifies the interpretation of results. The integration of these functions into a single tool eliminates the need for lengthy data handling and parsing, significantly expediting access to global patterns in the data.
Multi-label literature classification based on the Gene Ontology graph
Authors: Jin Bo , Muller Brian , Zhai Chengxiang , Lu Xinghua 
Published: December 2008

Abstract

Background
The Gene Ontology is a controlled vocabulary for representing knowledge related to genes and proteins in a computable form. The current effort of manually annotating proteins with the Gene Ontology is outpaced by the rate of accumulation of biomedical knowledge in literature, which urges the development of text mining approaches to facilitate the process by automatically extracting the Gene Ontology annotation from literature. The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification.

Results
In this research, we investigated the methods of enhancing automatic multi-label classification of biomedical literature by utilizing the structure of the Gene Ontology graph. We have studied three graph-based multi-label classification algorithms, including a novel stochastic algorithm and two top-down hierarchical classification methods for multi-label literature classification. We systematically evaluated and compared these graph-based classification algorithms to a conventional flat multi-label algorithm. The results indicate that, through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods can significantly improve predictions of the Gene Ontology terms implied by the analyzed text. Furthermore, the graph-based multi-label classifiers are capable of suggesting Gene Ontology annotations (to curators) that are closely related to the true annotations even if they fail to predict the true ones directly. A software package implementing the studied algorithms is available for the research community.

Conclusion
Through utilizing the information from the structure of the Gene Ontology graph, the graph-based multi-label classification methods have better potential than the conventional flat multi-label classification approach to facilitate protein annotation based on the literature.