Search Interfaces for Mathematicians

Access to mathematical knowledge has changed dramatically in recent years, therefore changing mathematical search practices. Our aim with this study is to scrutinize professional mathematicians' search behavior. With this understanding we want to be able to reason why mathematicians use which tool for what search problem in what phase of the search process. To gain these insights we conducted 24 repertory grid interviews with mathematically inclined people (ranging from senior professional mathematicians to non-mathematicians). From the interview data we elicited patterns for the user group "mathematicians" that can be applied when understanding design issues or creating new designs for mathematical search interfaces.Comment: conference article "CICM'14: International Conference on Computer Mathematics 2014", DML-Track: Digital Math Libraries 17 page

Mutations in HIV reverse transcriptase which alter RNase H activity and decrease strand transfer efficiency are suppressed by HIV nucleocapsid protein

Structural studies of authentic HIV reverse transcriptase (RT) suggest a role for the p51 carboxyl terminus in forming an active RNase H conformation [Rodgers, D. W., Gamblin, S. J., Harris, B. A., Ray, S., Culp, J. S., Hellmig, B., Woolf, D. J., Debouck, C. and Harrison, S.C. (1995) Proc. Natl. Acad. Sci. USA 92, 1222-1226]. We have purified mutant RT heterodimers containing deletion of 5, 9, or 13 amino acids from the p51 carboxyl terminus. These 'selectively deleted' heterodimers have been analyzed for changes in RNA-dependent DNA polymerase activity, RNase H activity, and the ability to catalyze DNA strand transfer. As deletions extended into the p51 subunit, a decrease in the stability of the RT-DNA complex was apparent. The largest effect was observed for p66/p51Δ13 RT, which showed a 3-fold decrease relative to wild-type RT. RNase H activity was measured by digestion of the RNA in a 5' 32P-labeled RNA/DNA hybrid. Deletion of 5 or 9 amino acids from pSI had little effect on synthesis-dependent and synthesis- independent RNase H activities. In contrast, deletion of 13 amino acids from p51 increased the length of the hydrolysis products of both RNase H activities by 8-10 bp, thus changing the spatial relationship between the polymerase and RNase H active sites from a distance of 17-18 bp to 26-27 bp. The Δ13 derivative was also incapable of efficient DNA strand transfer. This defect in strand transfer could be suppressed by the 71-amino acid form of HIV nucleocapsid protein (NC) but not by the 55-amino acid form (NC55) or by equine infectious anemia virus NC. These results provide evidence for the existence of a specific complex between RT and NC and are discussed in terms of the role of this complex in proviral DNA synthesis

Interferometric Bell-state preparation using femtosecond-pulse-pumped Spontaneous Parametric Down-Conversion

We present theoretical and experimental study of preparing maximally entangled two-photon polarization states, or Bell states, using femtosecond pulse pumped spontaneous parametric down-conversion (SPDC). First, we show how the inherent distinguishability in femtosecond pulse pumped type-II SPDC can be removed by using an interferometric technique without spectral and amplitude post-selection. We then analyze the recently introduced Bell state preparation scheme using type-I SPDC. Theoretically, both methods offer the same results, however, type-I SPDC provides experimentally superior methods of preparing Bell states in femtosecond pulse pumped SPDC. Such a pulsed source of highly entangled photon pairs is useful in quantum communications, quantum cryptography, quantum teleportation, etc.Comment: 11 pages, two-column format, to appear in PR

Assessing rates of parasite coinfection and spatiotemporal strain variation via metabarcoding: insights for the conservation of European turtle doves Streptopelia turtur

Understanding the frequency, spatiotemporal dynamics and impacts of parasite coinfections is fundamental to developing control measures and predicting disease impacts. The European turtle dove (Streptopelia turtur) is one of Europe's most threatened bird species. High prevalence of infection by the protozoan parasite Trichomonas gallinae has previously been identified, but the role of this and other coinfecting parasites in turtle dove declines remains unclear. Using a high-throughput sequencing approach, we identified seven strains of T. gallinae, including two novel strains, from ITS1/5.8S/ITS2 ribosomal sequences in turtle doves on breeding and wintering grounds, with further intrastrain variation and four novel subtypes revealed by the iron-hydrogenase gene. High spatiotemporal turnover was observed in T. gallinae strain composition, and infection was prevalent in all populations (89%–100%). Coinfection by multiple Trichomonas strains was rarer than expected (1% observed compared to 38.6% expected), suggesting either within-host competition, or high mortality of coinfected individuals. In contrast, coinfection by multiple haemosporidians was common (43%), as was coinfection by haemosporidians and T. gallinae (90%), with positive associations between strains of T. gallinae and Leucocytozoon suggesting a mechanism such as parasite-induced immune modulation. We found no evidence for negative associations between coinfections and host body condition. We suggest that longitudinal studies involving the recapture and investigation of infection status of individuals over their lifespan are crucial to understand the epidemiology of coinfections in natural populations

Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing. Alternatively, large dnCNVs are found likely to contain multiple modest-effect risk genes. Overall, we find strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, including 6 CNV regions (noted above) and 65 risk genes (FDR ≤ 0.1). Through analysis of de novo mutations in autism spectrum disorder (ASD), Sanders et al. find that small deletions, but not large deletions/duplications, contain one critical gene. Combining CNV and sequencing data, they identify 6 loci and 65 genes associated with ASD. © 2015 Elsevier Inc

Do distributions of diamondoid hydrocarbons accumulated in oil-contaminated fish tissues help to identify the sources of oil?

Identifying the sources of environmental oil contamination can be challenging, especially for oil in motile organisms such as fish. Lipophilic hydrocarbons from oil can bioaccumulate in fish adipose tissue and potentially provide a forensic “fingerprint” of the original oil. Herein, diamondoid hydrocarbon distributions were employed to provide such fingerprints. Indices produced from diamondoids were used to compare extracts from fish adipose tissues and the crude and fuel oils to which the fish were exposed under laboratory conditions. A suite of 20 diamondoids was found to have bioaccumulated in the dietary-exposed fish. Cross-plots of indices between fish and exposure oils were close to the ideal 1:1 relationship. Comparisons with diamondoid distributions of non-exposure oils produced overall, but not exclusively, weaker correlations. Linear Discriminatory Analysis on a combined set of 15 diamondoid and bicyclane molecular ratios was able to identify the exposure oils, so a use of both compound classes is preferable

Truncating α-Helix E′ of p66 human immunodeficiency virus reverse transcriptase modulates RNase H function and impairs DNA strand transfer

The properties of recombinant p66/p51 human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) containing C-terminal truncations in its p66 polypeptide were evaluated. Deletion end points partly or completely removed α-helix E′ of the RNase H domain (p66Δ8/p51 and p66Δ16/p51, respectively), while mutant p66Δ23/p51 lacked αE′ and the β5′-αE′ connecting loop. Although dimerization and DNA polymerase properties of all mutants were not significantly different from those of the parental enzyme, p66Δ16/p51 and p66Δ23/ p51 RT lacked ribonuclease H (RNase H) activity. In contrast, RT mutant p66Δ8/p51 retained endonuclease activity but lacked the directional processing feature of the parental enzyme. Despite retaining full endoribonuclease function, p66Δ8/p51 RT barely supported transfer of nascent (-)-strand DNA between RNA templates representing the 5′ and 3′ ends of retroviral genome, shedding light on the requirement for the endonuclease and directional processing functions of the RNase H domain during replication

Fish Fingerprinting: Identifying Crude Oil Pollutants using Bicyclic Sesquiterpanes (Bicyclanes) in the Tissues of Exposed Fish

In the present study, we investigated the possibility of identifying the source oils of exposed fish using ratios of bicyclic sesquiterpane (bicyclane) chemical biomarkers. In the event of an oil spill, identification of source oil(s) for assessment, or for litigation purposes, typically uses diagnostic ratios of chemical biomarkers to produce characteristic oil “fingerprints.” Although this has been applied in identifying oil residues in sediments, water, and sessile filtering organisms, so far as we are aware this has never been successfully demonstrated for oil-exposed fish. In a 35-day laboratory trial, juvenile Lates calcarifer (barramundi or Asian seabass) were exposed, via the diet (1% w/w), to either a heavy fuel oil or to Montara, an Australian medium crude oil. Two-dimensional gas chromatography with high-resolution mass spectrometry and gas chromatography–mass spectrometry were then used to measure selected ratios of the bicyclanes to examine whether the ratios were statistically reproducibly conserved in the fish tissues. Six diagnostic bicyclane ratios showed high correlation (r2 > 0.98) with those of each of the two source oils. A linear discriminatory analysis model showed that nine different petroleum products could be reproducibly discriminated using these bicyclane ratios. The model was then used to correctly identify the bicyclane profiles of each of the two exposure oils in the adipose tissue extracts of each of the 18 fish fed oil-enriched diets. From our initial study, bicyclane biomarkers appear to show good potential for providing reliable forensic fingerprints of the sources of oil contamination of exposed fish. Further research is needed to investigate the minimum exposure times required for bicyclane bioaccumulation to achieve detectable concentrations in fish adipose tissues and to determine bicyclane depuration rates once exposure to oil has ceased. Environ Toxicol Chem 2023;42:7–18. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC

ERP abnormalities of illusory contour perception in Williams Syndrome

Williams syndrome is a genetic disorder in which visuo-spatial performance is poor. Theorists have claimed that the deficit lies in high-level processing, leaving low-level visual processes intact. We investigated this claim by examining an aspect of low-level processing, perceptual completion, i.e. the ability of this clinical group to perceive illusory Kanizsa squares. We then used event-related potentials to examine neural correlates of perceptual completion. While participants were able to perceive illusory contours, the neural correlates of this apparently normal perception were different from controls. Such differences in low-level visual processes may significantly impact on the development of higher-level visual processes. We conclude that, contrary to earlier claims, there is atypical neural processing during low-level visual perception in Williams syndrome