Effects of zinc and fluoride on the remineralisation of artificial carious lesions under simulated plaque fluid conditions.

The aim was to study the effects of zinc (Zn) and fluoride (F) on remineralisation at plaque fluid concentrations. Artificial carious lesions were created in 2 acid-gel demineralising systems (initially infinitely undersaturated and partially saturated with respect to enamel) giving lesions with different mineral distribution characteristics (high and low R values, respectively) but similar integrated mineral loss values. Lesions of both types were assigned to 1 of 4 groups and remineralised for 5 days at 37°C. Zn and F were added, based on plaque fluid concentrations 1 h after application, to give 4 treatments: 231 μmol/l Zn, 10.5 μmol/l F, Zn/F combined and an unmodified control solution (non-F/non-Zn). Subsequently remineralisation was measured using microradiography. High-R lesions were analysed for calcium, phosphorus, F and Zn using electron probe micro-analysis. All lesions underwent statistically significant remineralisation. For low-R lesions, remineralisation was in the order F(a) < non-F/non-Zn(a) < Zn(a, b) < Zn/F(b), and for high-R lesions F(a) < non-F/non-Zn(b) < Zn(b) < Zn/F(c) (treatments with the same superscript letter not significantly different, at p < 0.05). Qualitatively, remineralisation occurred throughout non-F/non-Zn and Zn groups, predominantly at the surface zone (F) and within the lesion body (Zn/F). Electron probe micro-analysis revealed Zn in relatively large amounts in the outer regions (Zn, Zn/F). F was abundant not only at the surface (F), but also in the lesion body (Zn/F). Calcium:phosphate ratios were similar to hydroxyapatite (all). To conclude, under static remineralising conditions simulating plaque fluid, Zn/F treatment gave significantly greater remineralisation than did F treatment, possibly because Zn in the Zn/F group maintained greater surface zone porosity compared with F, facilitating greater lesion body remineralisation

Austro-Asiatic Tribes of Northeast India Provide Hitherto Missing Genetic Link between South and Southeast Asia

Northeast India, the only region which currently forms a land bridge between the Indian subcontinent and Southeast Asia, has been proposed as an important corridor for the initial peopling of East Asia. Given that the Austro-Asiatic linguistic family is considered to be the oldest and spoken by certain tribes in India, Northeast India and entire Southeast Asia, we expect that populations of this family from Northeast India should provide the signatures of genetic link between Indian and Southeast Asian populations. In order to test this hypothesis, we analyzed mtDNA and Y-Chromosome SNP and STR data of the eight groups of the Austro-Asiatic Khasi from Northeast India and the neighboring Garo and compared with that of other relevant Asian populations. The results suggest that the Austro-Asiatic Khasi tribes of Northeast India represent a genetic continuity between the populations of South and Southeast Asia, thereby advocating that northeast India could have been a major corridor for the movement of populations from India to East/Southeast Asia

The computational therapeutic: exploring Weizenbaum's ELIZA as a history of the present

This paper explores the history of ELIZA, a computer programme approximating a Rogerian therapist, developed by Jospeh Weizenbaum at MIT in the 1970s, as an early AI experiment. ELIZA’s reception provoked Weizenbaum to re-appraise the relationship between ‘computer power and human reason’ and to attack the ‘powerful delusional thinking’ about computers and their intelligence that he understood to be widespread in the general public and also amongst experts. The root issue for Weizenbaum was whether human thought could be ‘entirely computable’ (reducible to logical formalism). This also provoked him to re-consider the nature of machine intelligence and to question the instantiation of its logics in the social world, which would come to operate, he said, as a ‘slow acting poison’. Exploring Weizenbaum’s 20th Century apostasy, in the light of ELIZA, illustrates ways in which contemporary anxieties and debates over machine smartness connect to earlier formations. In particular, this article argues that it is in its designation as a computational therapist that ELIZA is most significant today. ELIZA points towards a form of human–machine relationship now pervasive, a precursor of the ‘machinic therapeutic’ condition we find ourselves in, and thus speaks very directly to questions concerning modulation, autonomy, and the new behaviorism that are currently arising

Identification and Characterization of Two Functionally Unknown Genes Involved in Butanol Tolerance of Clostridium acetobutylicum

Solvents toxicity is a major limiting factor hampering the cost-effective biotechnological production of chemicals. In Clostridium acetobutylicum, a functionally unknown protein (encoded by SMB_G1518) with a hypothetical alcohol interacting domain was identified. Disruption of SMB_G1518 and/or its downstream gene SMB_G1519 resulted in increased butanol tolerance, while overexpression of SMB_G1518-1519 decreased butanol tolerance. In addition, SMB_G1518-1519 also influences the production of pyruvate:ferredoxin oxidoreductase (PFOR) and flagellar protein hag, the maintenance of cell motility. We conclude that the system of SMB_G1518-1519 protein plays a role in the butanol sensitivity/tolerance phenotype of C. acetobutylicum, and can be considered as potential targets for engineering alcohol tolerance

Efficient counting of k-mers in DNA sequences using a bloom filter

<p>Abstract</p> <p>Background</p> <p>Counting <it>k</it>-mers (substrings of length <it>k </it>in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting <it>k</it>-mers in large modern sequence data sets can easily overwhelm the memory capacity of standard computers. In current data sets, a large fraction-often more than 50%-of the storage capacity may be spent on storing <it>k</it>-mers that contain sequencing errors and which are typically observed only a single time in the data. These singleton <it>k</it>-mers are uninformative for many algorithms without some kind of error correction.</p> <p>Results</p> <p>We present a new method that identifies all the <it>k</it>-mers that occur more than once in a DNA sequence data set. Our method does this using a Bloom filter, a probabilistic data structure that stores all the observed <it>k</it>-mers implicitly in memory with greatly reduced memory requirements. We then make a second sweep through the data to provide exact counts of all nonunique <it>k</it>-mers. For example data sets, we report up to 50% savings in memory usage compared to current software, with modest costs in computational speed. This approach may reduce memory requirements for any algorithm that starts by counting <it>k</it>-mers in sequence data with errors.</p> <p>Conclusions</p> <p>A reference implementation for this methodology, BFCounter, is written in C++ and is GPL licensed. It is available for free download at <url>http://pritch.bsd.uchicago.edu/bfcounter.html</url></p

Well-being outcomes of marine protected areas

Marine protected areas are advocated as a key strategy for simultaneously protecting marine biodiversity and supporting coastal livelihoods, but their implementation can be challenging for numerous reasons, including perceived negative effects on human well-being. We synthesized research from 118 peer-reviewed articles that analyse outcomes related to marine protected areas on people, and found that half of documented well-being outcomes were positive and about one-third were negative. No-take, well-enforced and old marine protected areas had positive human well-being outcomes, which aligns with most findings from ecological studies. Marine protected areas with single zones had more positive effects on human well-being than areas with multiple zones. Most studies focused on economic and governance aspects of well-being, leaving social, health and cultural domains understudied. Well-being outcomes arose from direct effects of marine protected area governance processes or management actions and from indirect effects mediated by changes in the ecosystem. Our findings illustrate that both human well-being and biodiversity conservation can be improved through marine protected areas, yet negative impacts commonly co-occur with benefits

The Effect of Testing on the Retention of Coherent and Incoherent Text Material

Research has shown that testing during learning can enhance the long-term retention of text material. In two experiments, we investigated the testing effect with a fill-in-the-blank test on the retention of text material. In Experiment 1, using a coherent text, we found no retention benefit of testing compared to a restudy (control) condition. In Experiment 2, text coherence was disrupted by scrambling the order of the sentences from the text. The material was subsequently presented as a list of facts as opposed to connected discourse. For the incoherent version of the text, testing slowed down the rate of forgetting compared to a restudy (control) condition. The results suggest that the connectedness of materials can play an important role in determining the magnitude of testing benefits for long-term retention. Testing with a completion test seems most beneficial for unconnected materials and less so for highly structured materials

Three options for citation tracking: Google Scholar, Scopus and Web of Science

BACKGROUND: Researchers turn to citation tracking to find the most influential articles for a particular topic and to see how often their own published papers are cited. For years researchers looking for this type of information had only one resource to consult: the Web of Science from Thomson Scientific. In 2004 two competitors emerged – Scopus from Elsevier and Google Scholar from Google. The research reported here uses citation analysis in an observational study examining these three databases; comparing citation counts for articles from two disciplines (oncology and condensed matter physics) and two years (1993 and 2003) to test the hypothesis that the different scholarly publication coverage provided by the three search tools will lead to different citation counts from each. METHODS: Eleven journal titles with varying impact factors were selected from each discipline (oncology and condensed matter physics) using the Journal Citation Reports (JCR). All articles published in the selected titles were retrieved for the years 1993 and 2003, and a stratified random sample of articles was chosen, resulting in four sets of articles. During the week of November 7–12, 2005, the citation counts for each research article were extracted from the three sources. The actual citing references for a subset of the articles published in 2003 were also gathered from each of the three sources. RESULTS: For oncology 1993 Web of Science returned the highest average number of citations, 45.3. Scopus returned the highest average number of citations (8.9) for oncology 2003. Web of Science returned the highest number of citations for condensed matter physics 1993 and 2003 (22.5 and 3.9 respectively). The data showed a significant difference in the mean citation rates between all pairs of resources except between Google Scholar and Scopus for condensed matter physics 2003. For articles published in 2003 Google Scholar returned the largest amount of unique citing material for oncology and Web of Science returned the most for condensed matter physics. CONCLUSION: This study did not identify any one of these three resources as the answer to all citation tracking needs. Scopus showed strength in providing citing literature for current (2003) oncology articles, while Web of Science produced more citing material for 2003 and 1993 condensed matter physics, and 1993 oncology articles. All three tools returned some unique material. Our data indicate that the question of which tool provides the most complete set of citing literature may depend on the subject and publication year of a given article

Long Term Protection after Immunization with P. berghei Sporozoites Correlates with Sustained IFNγ Responses of Hepatic CD8+ Memory T Cells

Protection against P. berghei malaria can successfully be induced in mice by immunization with both radiation attenuated sporozoites (RAS) arresting early during liver stage development, or sporozoites combined with chloroquine chemoprophylaxis (CPS), resulting in complete intra-hepatic parasite development before killing of blood-stages by chloroquine takes place. We assessed the longevity of protective cellular immune responses by RAS and CPS P. berghei immunization of C57BL/6j mice. Strong effector and memory (TEM) CD8+ T cell responses were induced predominantly in the liver of both RAS and CPS immunized mice while CD4+ T cells with memory phenotype remained at base line levels. Compared to unprotected naïve mice, we found high sporozoite-specific IFNγ ex vivo responses that associated with induced levels of in vivo CD8+ TEM cells in the liver but not spleen. Long term evaluation over a period of 9 months showed a decline of malaria-specific IFNγ responses in RAS and CPS mice that significantly correlated with loss of protection (r2 = 0.60, p<0.0001). The reducing IFNγ response by hepatic memory CD8+ T cells could be boosted by re-exposure to wild-type sporozoites. Our data show that sustainable protection against malaria associates with distinct intra-hepatic immune responses characterized by strong IFNγ producing CD8+ memory T cells