240 research outputs found
R19. Investigation of Taste Masking Efficiency of Caffeine Citrate by Lipids Utilizing Hot Melt Extrusion Technology
No full textCorresponding author (Pharmaceutics and Drug delivery): Priyanka Srinivasan, [email protected]://egrove.olemiss.edu/pharm_annual_posters/1018/thumbnail.jp
Tidal bores, catastrophic flooding in Bangladesh, and the potential usefulness of causeways
No full textThrough discussion of the worldwide devastation that tidal bores can cause, author Priyanka Joseph, examines the causes and the possible solutions to prevent these destructive waves. The pros and cons of each solution (such as causeways, viaducts, and regulators) are debated as well as their effect on the surrounding areas and environment
Suppressing Beam Background and Fake Photons at Belle II using Machine Learning
No full textThe Belle II experiment situated at the SuperKEKB energyasymmetric e+
e− collider began operation in 2019. It has since recorded half of the data collected by its predecessor, and reached a world record instantaneous luminosity of 4.7 × 1034 cm-2s-1. For distinguishing decays with missing energy from background events at Belle II, the residual calorimeter energy measured by the electromagnetic calorimeter is an important quantity. Ideally, calorimeter clusters due to beam backgrounds and fake photons should be excluded when the residual calorimeter energy is calculated, so identifying them during the analysis process is key. We present two new boosted decision tree classifiers that have been trained to identify such clusters at Belle II and distinguish them from real photons originating from collision events at the interaction point. We provide results from their application to the B → D*ℓν decay mode, and show that the distribution of residual calorimeter energy for signal events is significantly improved
Study of Marine Natural Products as Anti-SARS-CoV-2 Agents Using Molecular Modeling
No full textCorresponding author (BioMolecular Sciences): Priyanka Samanta, [email protected]://egrove.olemiss.edu/pharm_annual_posters_2022/1018/thumbnail.jp
Distributed human computation framework for linked data co-reference resolution
No full textDistributed Human Computation (DHC) is a technique used to solve computational problems by incorporating the collaborative effort of a large number of humans. It is also a solution to AI-complete problems such as natural language processing. The Semantic Web with its root in AI is envisioned to be a decentralised world-wide information space for sharing machine-readable data with minimal integration costs. There are many research problems in the Semantic Web that are considered as AI-complete problems. An example is co-reference resolution, which involves determining whether different URIs refer to the same entity. This is considered to be a significant hurdle to overcome in the realisation of large-scale Semantic Web applications. In this paper, we propose a framework for building a DHC system on top of the Linked Data Cloud to solve various computational problems. To demonstrate the concept, we are focusing on handling the co-reference resolution in the Semantic Web when integrating distributed datasets. The traditional way to solve this problem is to design machine-learning algorithms. However, they are often computationally expensive, error-prone and do not scale. We designed a DHC system named iamResearcher, which solves the scientific publication author identity co-reference problem when integrating distributed bibliographic datasets. In our system, we aggregated 6 million bibliographic data from various publication repositories. Users can sign up to the system to audit and align their own publications, thus solving the co-reference problem in a distributed manner. The aggregated results are published to the Linked Data Cloud
Search for the lepton flavour violating decay B0 -> ell tau at Belle II
No full textToday, numerous avenues are explored to search for any evidence of new physics beyond the
Standard Model, one of which is rare particle decays. Such decays are promising as their
suppressed decay rates allow for any enhancements from new physics contributions to be more
readily seen. One such rare decay of interest is B0 → ell tau (ell = e, μ) which is a lepton flavour
violating decay making it forbidden within the conventional Standard Model framework. However,
within an extended Standard Model that includes neutrino oscillations, which there is strong evidence
for, the decay can occur but at a rate far beyond any current or future experimental sensitivity.
Therefore, observation of B0 → ell tau would be strong and clear evidence of new physics beyond
the Standard Model. This study presents the first search for B0 → ell tau using 365/fb of data
collected by the Belle II experiment from 2019-2022. The Belle II experiment is situated around the
interaction point of the SuperKEKB collider which is an asymmetric e+e− collider designed to mass
produce B mesons. The primary aim of the study presented in this thesis is to develop an analysis
technique for future hadronic tag-based B0 → ell tau searches at Belle II that yields an improved
sensitivity over previous analysis strategies employed by other experiments. This is achieved by
partitioning the tau decay into leptonic and hadronic modes, and designing separate signal extraction
methods that are optimised for each as opposed to employing a global strategy for all tau decays.
Focusing only on the leptonic tau decays for now, upper limits on the B0 → ell tau branching fraction
are derived using a hybrid cut-and-count approach based on the Rolke-Lopez interval method. The
results from just the leptonic tau decays have a sensitivity that is competitive with the current worldleading
upper limits using only a fraction of the dat
Cenchrus ciliaris RepeatExplorer Priyanka Rathore, Bhat, Schwarzacher, Heslop-Harrison, Tomaszewska
No full textThe repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris Abstract
RepeatExplorer supplementary data for manuscript:
Priyanka Rathore1, Paulina Tomaszewska[H(1] [ST(2] 2,3, Trude Schwarzacher2,4, J.S. (Pat) Heslop-Harrison2,4,* and Vishnu Bhat1
1)Department of Botany, Faculty of Science, University of Delhi, Delhi, India
2)Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
3)Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, 50-328 Wrocław, Poland
4)Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
*)Corresponding author. E-mail: [email protected] and [email protected]
Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in tropical and subtropical regions of Africa and Asia. In this work, we aim to investigate the genomic organization and characterize the nature of repetitive DNA sequences in this species. Because of the apomictic propagation, various aneuploid genotypes are found and we analysed here a 2n=4×+3=39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. About a third of Ty1-copia sites overlapped or spanned centromeric DAPI positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methycytosine signals, except some Ty3-gypsy on the arms of chromosomes which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. Developed Cluster probes gave strong signals mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris likely having different repeat sequence variants amplified before the genome came together in the tetraploid.
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How can we use Livework's approach to org change for CC for SF?: A tool for Livework to enable organisations to think in sustainable and thriving systems
No full textAs sustainability becomes one of the critical topics of our times, organisations seek guidance on feasible and pragmatic ways to implement the same. To reduce the know-do gap, the thesis collaboration between Livework and the Technical University of Delft explores the problem statement: How can we use Livework’s service architecture approach for organisational change for customer-centricity (CC) for Sustainable futures (SF)? Empirical research and semi-structured qualitative interviews focus on two main areas of focus: 1. Livework’s service architecture approach; and 2. Sustainable futures. The results and findings of the interviews with Livework employees, their clients and five sustainability leaders in organisations led to defining a vision for Livework and a set of goals and objectives. To make the vision a reality a roadmap is designed. Turning the vision into action, the tool workshop: organisation as a garden is designed. The workshop imagines an organisation like a garden, where the soil a.k.a the core of the business has to thrive with a network of nurturers and influencers. Using this tool in a collaborative manner with organisations, Livework learns about their mindset, pain points and scope a plan of action to enable them to think in regenerative and thriving systems.Strategic Product Desig
Structural characterization of spray-dried microgranules by spin-echo small-angle neutron scattering
No full textSpray-drying is a widely used industrial technique and has shown an immense potential in the fields of nanoscience and technology. This is due to its ability to synthesize microgranules consisting of correlated nanostructures using evaporation induced assembly through bottom-up approach. Although the nature of correlation among the constituent nanoparticles and their size distribution could earlier be obtained by conventional Small-angle Scattering (SAS) technique, a statistically averaged quantitative measure of the shell thickness and hollowness of the formed granules remained a challenge. In this work, we have used Spin-echo Small-angle Neutron Scattering (SESANS) technique to characterize spray-dried nanostructured microgranules having different hollowness. It is shown that this non-destructive technique provided precise quantification of the granular sizes and hollowness by utilizing polarization property of neutrons in real space directly.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.RST/Neutron and Positron Methods in Material
PREreview of "Mutational Profiling of SARS-CoV-2 PLpro in human cells reveals requirements for function, structure, and drug escape"
No full text<p><strong>This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at <a href="https://prereview.org/reviews/11130669">https://prereview.org/reviews/11130669</a>.</strong></p>
<p><b>Summary:</b></p><p>In this study the authors comprehensively examined the mutational effects on PLpro proteolytic activity and stability. The authors have designed a FRET-based assay composed of N-terminal mClover3 donor and C-terminal m-Ruby3 acceptor fluorophores separated by a linker containing the Nsp2/3 PLpro cleavage motif to measure the proteolytic activity of PLpro. From DMS data the authors infer PLpro active site mutations ablates activity. Their study also revealed residues required for cleavage of the Nsp2/3 site, identified features of substrate binding pocket and the sequence requirements of the blocking loop. The authors have given explanations for their observations in the Discussion section. Overall, the paper is supported with follow-up enzymology and crystallography experiments of key residues. The major limitation of this study is leaky expression of mutations can mask clinically relevant mutations that can arise due to viral evolution and might have the potential to evade inhibitor treatment. Study of such mutations can provide more information about the potential escape routes open to the virus to evade developing therapeutics. Moreover, incorporation of statistical analysis could strengthen the confidence in inferences drawn from the deep sequencing data and improve the quality of the manuscript. </p><p>The following points can improve the quality of the manuscript:</p><p><b>Major points:</b></p><p>1. In Figure 1f, it is unclear that why is the PLpro activity increasing with increase in inhibitor concentration? Perhaps the Y axis is mislabeled as while inhibitor concentration is increasing, PLpro activity should decrease. However, FRET signal would increase (and maybe should be the axis label), since there will be no cleavage. </p><p>2. Line 175 – 178 - What does 0 represent in the normalized dataset? What is the rationale used for selecting minimum 10 reads in the unselected library as the read cut-off. 10 reads is pretty low cut-off. From the data, it seems the distribution tails off before cut-off chosen for the s.d.- by eye. 0.3 s.d and 20 as read cut-off might be a better option to eliminate sequencing artifacts.</p><p>3. Line 187-190 – What is the number of reads for the mutants that showed lower activity scores? There is a possibility that due to low read cutoff, these mutants might be lying in the range with low reads in the unselected library.</p><p>4. Line 223-224 – Authors mention they find a good correlation between activity and abundance score. Although this is noticeable from the scatter plot but supporting high-throughput data with statistical parameters like pearson correlation coefficient, a metric that provides comparison between 2 datasets will make this data reporting more quantitative and informative.</p><p>5. Line 1340- Figure 3b- What do authors mean by variants with small enough error? Please be precise.</p><p>6. Line 315-319/ Line 1550-1556- Extended data Fig 15c – It is difficult to interpret the inference reported that is based on the data in Extended Fig 15. There is no data reported for Normalized AMC cleavage for Y268W. Interpretation can be more comprehensible by plotting a scatter plot between the Normalized Activity Fitness Scores obtained from DMS data and Normalized AMC cleavage (%). Through this plot, the reader can easily make out the outlier.</p><p>7. Line 364-367 – Authors mention "M208W strikingly increases the protein melting temperature by over 5C, indicating a substantial improvement in thermal stability. Increased stability, and thus reduced turnover in cells, may provide a mechanism to explain leaky expression in our cellular assay and increased yield of recombinant protein for E.coli expression." Since, leaky expression is a different issue, it is confusing why will leaky expression be a plausible reason for increased stability but less activity? </p><p>8. Since Extended data Fig 11a shows that variants display substantial amount of leaky expression, how have the authors taken this information into account while inferring results from DMS activity scores, especially since they are quantifying at the RNA level and not at the DNA level? Can the activity scores obtained for the mutants be normalized to leaky expression scores in some way, for example by subtracting the scores obtained from the leaky expression dataset in order to measure the true activity of each mutant?</p><p>9. Solvents are known to affect an enzyme's activity, selectivity and stability. In Figure 5, authors should consider and comment about the role of solvent in understanding the mechanism of Michelis-Menten kinetics of M208 variants using substrates Z-RLRGG-AMC, Ubiquitin-Rhodamine and ISG15-Rhodamine.</p><p> <b>Minor points:</b></p><p>1. Figure numbers need to be reformatted. Figure 3 onwards they are incorrectly labelled. For eg. 'Fig 3' is labelled as 'Fig 1'.</p><p>2. Line 426-429 – In Figure 3b, L and R domains of papain should be labelled or highlighted in separate colors for the ease of understanding for the reader.</p><p>3. Overall, different DMS datasets obtained from different assays in the paper have different read cut-offs such as 10, 13 and 18. A consistent statistical logic for obtaining different read cut-offs across different DMS datasets will be helpful. Also, increasing the read cut-off might improve the data quality and minimize sequencing artefacts.</p><ul><li><p><b>Reviewed by Priyanka Bajaj and James Fraser</b></p></li></ul>
<h2>Competing interests</h2>
<p>The authors declare that they have no competing interests.</p>
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