bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conversational coordination: Collaboration for effective communication
Authors: Ricard Richard J. 
Published: December 2008

ABSTRACTThis investigation focused on early school-aged children's ability to negotiate shared reference in a task-oriented communication game. Conversational partners worked together on initiating and refining mutually acceptable referential labels for a series of abstract figures. Each child participated as both a sender and a matcher. In Experiment 1, developmental trends in the use of conversational strategies such as utterance-contingent queries, acknowledgments, and negations were observed. However, communicative efficiency was disrupted when the children switched dyadic roles. They reintroduced figures with novel labels when switching to a speaking role from a previous matching role, and vice versa. In Experiment 2, communicative efficiency was again disrupted at the point of role switch, even when the children were given feedback designed to minimize cross-role inconsistency. Interestingly, in both experiments, communicative inefficiency did not reduce a dyad's overall communicative success. These results suggest that, while children are in the process of learning how best to coordinate the use of conversational strategies and procedural rules, they still manage effective communication, albeit with a little extra effort.
Clinical evaluation of the effects of radiotherapy on oral mucosa and gingiva
Authors: Taheri M. , Sohrabi K. , Salehi M.H. , Najafi M.H. 
Published: December 2008

AbstractIntroduction:The use of radiotherapy, alone or in conjunction with surgical resection, is common in treating head and neck tumours. However, ionising radiation induces unavoidable changes in the surrounding normal tissues, causing severe complications. Therefore, we decided to study different effects of radiotherapy on gingiva and oral mucosa.Methods and Materials:This prospective analytical study was performed on 30 patients with head and neck cancers referred to the radiotherapy department of Ghaem Hospital from March to October 2006. Data were collected by means of interviews, clinical examinations and patients’ medical file investigation. The impact of different dosages of radiation on gingiva and oral mucosa was investigated. Data analysis was performed using general linear model (GLM), Cochran and multivariate analysis of variance (MANOVA) tests via SPSS V. 11.5 software.Results:A direct relationship between increase in radiation dosage, irritation of oral mucosa, ulcer development and mucositis was observed. But there was no significant relationship between NUG (necrotising ulcerative gingivitis) and perlèche and radiation dosage. Periodontal index (PI), gingival index (GI) and papillary bleeding index (PBI) were increased, but due to limited time of study (6–7 weeks), no change in gingival recession was observed. Plaque index (PLI) decreased during treatment process because of oral hygiene instructions.Conclusion:The oral and periodontal health status of head and neck cancer patients before and during radiotherapy has been described in this article. The authors believe that prevention or reduction of side-effects of radiation should be an integral part of treatment as they may have tremendous effect on the patient's quality of life. This study supports the need for dental assessment and treatment planning before radiation therapy.
Peripheral blood lymphocyte counts during standard conformal radiotherapy and TomoTherapy/IMRT for prostate cancer
Authors: Elsworthy M. , Plowman P.N. 
Published: December 2008

AbstractLymphopaenia is the earliest and the most sensitive routinely assessed biological parameter of corporeal radiation exposure in clinical practice; bone marrow, lymph nodes and peripheral blood lymphocyte populations are also at risk. During radical prostate radiotherapy, in 28 patients, the mean peripheral lymphocyte count fell from 1.76 × 109/l (standard deviation (SD) 0.63, 95% confidence interval (conf.) 0.23) to 1.10 × 109/l (SD 0.38, conf. 0.14), (p < 0.05). The question was asked as to whether intensity-modulated radiation therapy (IMRT) by TomoTherapy would cause more lymphopaenia than three-field conformal radiotherapy, bearing in mind the ‘low dose bath’ effect of IMRT and the long ‘beam-on’ times. Thirteen patients receiving three-field conformal radiotherapy experienced a fall in peripheral lymphocyte counts from 2.02 (SD: 0.62. conf. 0.43) to 1.17 × 109/l (SD: 0.47, conf. 0.26) after 34–38 Gy, as compared to a fall from 1.6 × 109/l (SD: 0.6, conf. 0.35) to 1.04 × 109/l (SD: 0.3, conf. 0.15) for 15 TomoTherapy patients—non-significant differences. We conclude that for this (approximately) standard, small-volume pelvic radiotherapy and to the dose under scrutiny, we cannot detect differences between the two radiotherapy techniques in terms of the lymphopaenia accruing. Neutrophil counts were similarly non-significantly different.
Prospective cohort survey of patient satisfaction with on-treatment review by advanced practice urology radiographer
Authors: Treeby Jo 
Published: December 2008

ABSTRACTRadiographers are undertaking roles that are a development and extension of what has traditionally been seen as their remit. As with any development, it is important that such changes in practise have a positive rather than negative effect on patient care and patient experience. This article examines patient perception and level of patient satisfaction of an ‘on-treatment review’ conducted by a site-specific advanced practitioner radiographer instead of an oncology doctor. Overall, the results were positive suggesting that such reviews, when conducted by an appropriately trained individual, can enhance patient care and provide a satisfactory level of support during treatment.
An audit of a radiotherapy review clinic for breast cancer patients: a multi-disciplinary approach
Authors: Cameron J.L. , Blyth C.M. , Kirby A.S. 
Published: December 2008

AbstractPurpose: With the advent of multi-disciplinary team working in Oncology practice, this audit was designed to assess patient satisfaction with this approach within an on-treatment review clinic for breast cancer patients. It also aimed to look at conformity of reporting of treatment side effects between different staff groups.Patients and methods: A questionnaire was distributed to 230 radical breast cancer patients once a week after each review clinic. An oncologist and a radiographer or nurse reviewed the patients during weeks 1–4 of treatment. A review form was completed at each visit specifying any side effects noted.Results: Patients appeared satisfied with their clinic visits to both the radiographer and nurse with 84 and 85% confidence and trust in the members of staff compared to 73% with the doctor. There was disparity in the recording of side effects between non-medical and medical staff groups.Conclusion: This audit has provided good evidence to support the continuation of multi-disciplinary review clinics. A key benefit is the reduction in clinic waiting times for patients and a substantial time saving for the medics. It also supports role development for the radiographer and nurse involved.
Open Source Drug Discovery
Authors: Yadav Jyoti , Consortium OSDD 
Published: December 2008

AbstractTuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected with TB bacilli every second. Overall, one-third of the world's population is currently infected with the TB bacillus. Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome sequence of the causative pathogen Mycobacterium tuberculosis was published about a decade ago and many years of painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting protection. Despite increasing investment, led by charities including the Gates Foundation, no novel drugs for TB have entered the market for many years.Novel mechanisms for attracting funding, particularly private sector funding, into this research area are desperately needed. We wish to bring in the power of genomics, computational technologies and participation of young and brilliant talent from Universities and Industrial partners with a strong inclination to apply a concerted effort to address this important scourge. All researchers contribute data on tuberculosis drug targets and active molecules through a copyleft agreement; anyone who is prepared to keep to this may participate. All the data is Clickwrap protected and credit sharing will be based on a novel and flexible micro-attribution system. This system is aimed at providing due credit through an active process. Various levels of investigators shall have appropriate levels of rights, recognition and responsibilities.Another valuable aspect is the partnerships of Industry with belief in Open Source systems and models. We name this concerted effort to tackle this dreaded disease as Open Source Drug Discovery for Tuberculosis.
Integrated Management of Gummy Stem Blight of Watermelon by Green Manure and Melcast-scheduled Fungicides
Authors: Zhou Xin-Gen , Everts Kathryne L. 
Published: December 2008

Watermelon gummy stem blight (GSB) management using a green manure cover crop, the weather-based disease forecasting program ‘Melcast,’ and bio- and reduced-risk fungicides was evaluated in Maryland. Soil incorporation of hairy vetch winter cover crop suppressed percent foliage affected by GSB in comparison to winter fallow in three of five trials conducted in 2004 and 2005. Programs of Reynoutria sachalinensis, Bacillus subtilis, or harpin protein applied in rotation with chlorothalonil provided control of GSB as effectively as did EBDC, boscalid, or cyprodinil plus fludioxonil. However, the bio-fungicide programs did not perform as well as chlorothalonil alternated with pyraclostrobin plus boscalid in 2005. Melcast-scheduled sprays of B. subtilis in rotation with chlorothalonil resulted in an average of 73% less synthetic fungicide applied to watermelon. However, GSB reduction in the B. subtilis program, although similar in 2005, was less that that obtained with chlorothalonil alone in 2004. These results suggest that the combined use of green manure with Melcast-scheduled fungicide applications could effectively manage GSB and reduce fungicide use. Biofungicides alternated with chlorothalonil also minimized use of synthetic fungicides and were effective under some conditions, but should be used with caution. Accepted for publication 22 September 2008. Published 20 November 2008.
The Demosponge Amphimedon queenslandica: Reconstructing the Ancestral Metazoan Genome and Deciphering the Origin of Animal Multicellularity
Authors: Degnan Bernard M. , Adamska Maja , Craigie Alina , Degnan Sandie M. , Fahey Bryony , Gauthier Marie , Hooper John N.A. , Larroux Claire , Leys Sally P. , Lovas Erica , Richards Gemma S. 
Published: December 2008

INTRODUCTIONSponges are one of the earliest branching metazoans. In addition to undergoing complex development and differentiation, they can regenerate via stem cells and can discern self from nonself (“allorecognition”), making them a useful comparative model for a range of metazoan-specific processes. Molecular analyses of these processes have the potential to reveal ancient homologies shared among all living animals and critical genomic innovations that underpin metazoan multicellularity. Amphimedon queenslandica (Porifera, Demospongiae, Haplosclerida, Niphatidae) is the first poriferan representative to have its genome sequenced, assembled, and annotated. Amphimedon exemplifies many sessile and sedentary marine invertebrates (e.g., corals, ascidians, bryozoans): They disperse during a planktonic larval phase, settle in the vicinity of conspecifics, ward off potential competitors (including incompatible genotypes), and ensure that brooded eggs are fertilized by conspecific sperm. Using genomic and expressed sequence tag (EST) resources from Amphimedon, functional genomic approaches can be applied to a wide range of ecological and population genetic processes, including fertilization, dispersal, and colonization dynamics, host-symbiont interactions, and secondary metabolite production. Unlike most other sponges, Amphimedon produce hundreds of asynchronously developing embryos and larvae year-round in distinct, easily accessible brood chambers. Embryogenesis gives rise to larvae with at least a dozen cell types that are segregated into three layers and patterned along the body axis. In this article, we describe some of the methods currently available for studying A. queenslandica, focusing on the analysis of embryos, larvae, and post-larvae.
Dictyostelium discoideum: The Social Ameba
Authors: Gaudet Pascale , Fey Petra , Chisholm Rex 
Published: December 2008

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a “social ameba” because it can form a multicellular structure when nutrient conditions are limiting. D. discoideum and related organisms, known as the Dictyostelia, have been studied for almost 150 years. The cellular and molecular aspects of their multicellular lifestyle have been studied in detail, and general principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from this work and have been found to be conserved across all eukaryotes. The bacteriovore nature of the unicellular stage provides an excellent model in which to study phagocytosis and the mechanisms of bacterial virulence. D. discoideum has also been used successfully to explore the molecular basis of various human diseases, as well as the mechanisms of drug action and the pathways that lead to resistance to certain therapeutic agents. The availability of a complete genome sequence has further widened the scope of studies using D. discoideum. A large potential for secondary metabolism has become apparent, which opens the door to discovering new compounds with potential medical applications. Numerous putative orthologs of genes responsible for diseases in humans, but whose molecular functions are still uncharacterized, are present in the D. discoideum genome. Finally, the availability of community resources, including the genome database dictyBase and the Dicty Stock Center, makes D. discoideum an easily accessible and powerful model organism to study.
The Dogfish Scyliorhinus canicula: A Reference in Jawed Vertebrates
Authors: Coolen Marion , Menuet Arnaud , Chassoux Danièle , Compagnucci Claudia , Henry Sébastien , Lévèque Laurent , Da Silva Corinne , Gavory Frédérick , Samain Sylvie , Wincker Patrick , Thermes Claude , D’Aubenton-Carafa Yves , Rodriguez-Moldes Isabel , Naylor Gavin , Depew Michael , Sourdaine Pascal , Mazan Sylvie 
Published: December 2008

INTRODUCTIONDue to their large size and long generation times, chondrichthyans have been largely ignored by geneticists. However, their key phylogenetic position makes them ideal subjects to study the molecular bases of the important morphological and physiological innovations that characterize jawed vertebrates. Such analyses are crucial to understanding the origin of the complex genetic mechanisms unraveled in osteichthyans. The small spotted dogfish Scyliorhinus canicula, a representative of the largest order of extant sharks, presents a number of advantages in this context. Due to its relatively small size among sharks, its abundance, and easy maintenance, the dogfish has been an important model in comparative anatomy and physiology for more than a century. Recently, revived interest has occurred with the development of large-scale transcriptomic and genomic resources, together with the establishment of facilities allowing massive egg and embryo production. These new tools open the way to molecular analyses of the elaborate physiological and sensory systems used by sharks. They also make it possible to take advantage of unique characteristics of these species, such as organ zonation, in analyses of cell proliferation and differentiation. Finally, they offer important perspectives to evolutionary developmental biology that will provide a better understanding of the origin and diversifications of jawed vertebrates. The dogfish whole-genome sequence, which may shortly become accessible, should establish this species as an essential shark reference, complementary to other chondrichthyan models. These analyses are likely to reveal an organism of an underestimated complexity, far from the primitive prototypical gnathostome anticipated in gradistic views.
Bone Marrow-Derived Macrophages (BMM): Isolation and Applications
Authors: Weischenfeldt Joachim , Porse Bo 
Published: December 2008

INTRODUCTIONBone marrow-derived macrophages (BMM) are primary macrophage cells, derived from bone marrow cells in vitro in the presence of growth factors. Macrophage colony-stimulating factor (M-CSF) is a lineage-specific growth factor that is responsible for the proliferation and differentiation of committed myeloid progenitors into cells of the macrophage/monocyte lineage. Mice lacking functional M-CSF are deficient in macrophages and osteoclasts and suffer from osteopetrosis. In this protocol, bone marrow cells are grown in culture dishes in the presence of M-CSF, which is secreted by L929 cells and is used in the form of L929-conditioned medium. Under these conditions, the bone marrow monocyte/macrophage progenitors will proliferate and differentiate into a homogenous population of mature BMMs. The efficiency of the differentiation is assessed using fluorescence-activated cell sorting (FACS) analysis of Mac-1 and 4/80 surface antigen expression. Once differentiated, the BMMs are suitable for numerous types of experimental manipulations, including morphological, gene expression, and physiological studies. For example, phagocytic cells such as macrophages have a unique ability to ingest microbes. We describe a test for the phagocytic efficiency of BMMs by exposing them to fluorescently labeled yeast zymosan bioparticles. Also, a method to deliver DNA or small interfering RNAs (siRNAs) into these hard-to-transfect cells is described. Finally, the proliferation of the BMMs is assayed using carboxyfluorescein succinimidyl ester (CFSE), a fluorescein derivative that partitions equally between daughter cells after cell division.
Isolation of Amphimedon Developmental Material
Authors: Leys Sally P. , Larroux Claire , Gauthier Marie , Adamska Maja , Fahey Bryony , Richards Gemma S. , Degnan Sandie M. , Degnan Bernard M. 
Published: December 2008

INTRODUCTIONFertilization occurs internally in Amphimedon and embryos are brooded in multiple chambers throughout the adult. Each chamber contains a mixture of developmental stages, from egg to late ring stages (i.e., prehatch late embryos). At the end of embryogenesis, swimming parenchymella larvae emerge from the adult. After several hours in the water column, the larvae settle and metamorphose into juvenile sponges. This protocol details how to obtain Amphimedon larvae and post-larvae/juveniles as well as embryos. Once isolated, these biological stages can be used for a variety of molecular and cellular analyses.
Selection of Dictyostelium Transformants
Authors: Gaudet Pascale , Fey Petra , Chisholm Rex 
Published: December 2008

INTRODUCTIONDictyostelium discoideum is a unicellular eukaryote often referred to as a social ameba because it can form a multicellular structure when nutrient conditions are limiting. General principles for cell-to-cell communication, intracellular signaling, and cytoskeletal organization during cell motility have been derived from cellular and molecular studies of Dictyostelium and have been found to be conserved across all eukaryotes. The availability of a complete genome database and stocks of wild-type and mutant strains make D. discoideum an accessible and powerful model organism. Dictyostelium is amenable to genetic manipulations that require the introduction of DNA into cells, such as gene knockout, overexpression, antisense RNA expression, RNA interference (RNAi)-mediated gene knockdown, and restriction-enzyme-mediated mutagenesis. Two commonly used methods for DNA-mediated transformation in Dictyostelium are calcium phosphate precipitation and electroporation. Transformants can then be selected in liquid media or on bacterial plates. The latter method reduces the chances of contamination because the cells are grown in buffered agar containing live or dead bacteria, rather than in a rich broth. This method also facilitates the isolation of clones from transformations because each transformant produces a single colony on the plate instead of the pools of transformants obtained in liquid culture. For gene ablation experiments, it is important to obtain a minimum of two independent clones with the same phenotype to exclude the possibility that the phenotype is due to a nonspecific mutation.
Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions. Protocol 1: Coexpression of Query Protein on NAPPA Slides
Authors: Link Andrew J. , LaBaer Joshua 
Published: December 2008

INTRODUCTIONThe Nucleic Acid Programmable Protein Array (NAPPA) approach for producing protein microarrays uses cell-free extracts to transcribe and translate cDNAs encoding target proteins directly onto glass slides. Following array preparation, interactions with a protein of interest (query protein) are detected either by probing an expressed NAPPA slide with the purified query protein or by coexpressing the query protein on the NAPPA slide at the same time that the target proteins are expressed. This protocol describes the coexpression method, which involves adding the gene for the query protein to the cell-free protein expression mix. The amount of query protein that is transcribed and translated from the corresponding plasmid DNA depends on the amount of plasmid DNA used and the size of the protein of interest, among other factors. If too little query protein is expressed, there may be no detectable binding signal. Excessive amounts of protein expression may generate nonspecific background signals. Because the optimum amount of query plasmid varies with each query protein, it is essential to assess empirically the optimal amount of query protein DNA to add to a coexpression experiment.
Using the Nucleic Acid Programmable Protein Array (NAPPA) for Identifying Protein-Protein Interactions. Protocol 2: Detection of Query Proteins on NAPPA Slides
Authors: Link Andrew J. , LaBaer Joshua 
Published: December 2008

INTRODUCTIONThe Nucleic Acid Programmable Protein Array (NAPPA) approach for producing protein microarrays uses cell-free extracts to transcribe and translate cDNAs encoding target proteins directly onto glass slides. Identification of protein interactions can be accomplished either by probing an expressed NAPPA slide with a purified protein of interest (the query protein) or by coexpressing the query protein on the NAPPA slide at the same time that the target proteins are expressed. This protocol describes detection of query protein following coexpression of the query protein on the NAPPA array.