cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Design of a multi-epitope-based peptide vaccine against the SARS-CoV-2 Omicron variant using bioinformatics approach
Creators: name: Basmenj, Esmaeil Roohparvar
name: Omidvar, Behnoosh
name: Kiumarsy, Armity
name: Izadkhah, Habib
name: Ghiabi, Shamim
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Medicine
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: SARS-CoV-2, a member of the coronavirus family, is an RNA virus characterized by a single-stranded genome and is responsible for the development of COVID-19. The emergence of the Omicron variant of SARS-CoV-2 in 2021 marked a significant variation recognized by the World Health Organization. The primary objective of this study is to investigate the spike glycoprotein of the Omicron variant of SARS-CoV-2 and identify potential immunogenic epitopes in order to design multi-epitope vaccine constructs. Among the other major structural proteins of the coronavirus, the spike glycoprotein stands out as the largest. Importantly, individuals who have recovered from SARS-CoV-2 and COVID-19 were found to possess antibodies that target the spike glycoprotein. This article asserts that the vaccine presented in this study has the potential to elicit immune responses against previous variants, including the Omicron variant, as well as future variations. This is attributed to the utilization of a Java-based tool, which facilitated the identification of conserved epitopes with high immunogenicity scores, ensuring their non-toxic and non-allergenic properties. Our analysis provides strong evidence for the conservation of these epitopes across all coronavirus sequences detected in various countries since the beginning of the pandemic. The vaccine was subsequently constructed by integrating the identified conserved epitopes with linkers and adjuvants. The vaccine was subsequently evaluated through computational tests to assess their efficacy and performance. Communicated by Ramaswamy H. Sarma
Internalization of multiple cells during C. elegans gastrulation depends on common cytoskeletal mechanisms but different cell polarity and cell fate regulators
Creators: name: Goldstein, Bob
name: Harrell, Jessica R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: Understanding the links between developmental patterning mechanisms and force-producing cytoskeletal mechanisms is a central goal in studies of morphogenesis. Gastrulation is the first morphogenetic event in the development of many organisms. Gastrulation involves the internalization of surface cells, often driven by the contraction of actomyosin networks that are deployed with spatial precision -- both in specific cells and in a polarized manner within each cell. These cytoskeletal mechanisms rely on different cell fate and cell polarity regulators in different organisms. C. elegans gastrulation presents an opportunity to examine the extent to which diverse mechanisms may be used by dozens of cells that are internalized at distinct times within a single organism. We identified 66 cells that are internalized in C. elegans gastrulation, many of which were not known previously to gastrulate. To gain mechanistic insights into how these cells internalize, we genetically manipulated cell fate, cell polarity and cytoskeletal regulators and determined the effects on cell internalization. We found that cells of distinct lineages depend on common actomyosin-based mechanisms to gastrulate, but different cell fate regulators, and, surprisingly, different cell polarity regulators. We conclude that diverse cell fate and cell polarity regulators control common mechanisms of morphogenesis in C. elegans. The results highlight the variety of developmental patterning mechanisms that can be associated with common cytoskeletal mechanisms in the morphogenesis of an animal embryo.
title: Longitudinal density monitor for the LHC
Creators: name: Jeff, A
name: Andersen, M
name: Boccardi, A
name: Bozyigit, S
name: Bravin, E
name: Lefevre, T
name: Rabiller, A
name: Roncarolo, F
name: Welsch, CP
name: Fisher, AS
Publisher: name: University of Liverpool Repository
Year: 2013

description: The longitudinal density monitor (LDM) is primarily intended for the measurement of the particle population in nominally empty rf buckets. These so-called satellite or ghost bunches can cause problems for machine protection as well as influencing the luminosity calibration of the LHC. The high dynamic range of the system allows measurement of ghost bunches with as little as 0.01% of the main bunch population at the same time as characterization of the main bunches. The LDM is a single-photon counting system using visible synchrotron light. The photon detector is a silicon avalanche photodiode operated in Geiger mode, which allows the longitudinal distribution of the LHC beams to be measured with a resolution of 90ps. Results from the LDM are presented, including a proposed method for constructing a 3-dimensional beam density map by scanning the LDM sensor in the transverse plane. In addition, we present a scheme to improve the sensitivity of the system by using an optical switching technique. © 2012 American Physical Society.
Anomaly of the Internal Friction in the Helium Crystals Grown in the Burst-like Growth Mode
Creators: name: Tsymbalenko, V. L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The internal friction in the crystals grown in two modes, namely, slow and anomalously fast (burst-like growth) modes, is measured in the temperature range 0.49-0.75K at a frequency of about 75kHz. An additional contribution to the damping decrement and softening of the dynamic modulus are detected, and their relaxation to equilibrium values at a time constant of about 3ms is observed. Possible origins of this effect are discussed.
description: 7 pages, 5 figures
title: For neither love nor money: was the Flexible New Deal a more effective and efficient active labour market policy than those it replaced?
Creators: name: Davies, William
Publisher: name: University of Liverpool Repository
Year: 2013

description: Long-term unemployment creates a series of individual, social, and economic problems. Long-term unemployment has been treated with a wide variety of public policies: this thesis focuses on one approach - active labour market policies. Active labour market policies in the UK have emerged in stages, as the welfare state has incrementally evolved from a largely state-dominated and passive social security system to a market-led, work-first system where an escalating percentage of benefit recipients are expected to be actively seeking work. The theory and evidence underpinning these developments are explored in the first fives chapters. In the last decade, British governments have sought the assistance of private and voluntary sector organisations in the delivery of active labour market policies, using a system of payment-by-results to encourage these organizations to move individuals into, and sustain, employment. These are the core features underpinning the case study of this thesis, the Flexible New Deal. The Flexible New Deal is a programme for all long-term unemployed persons, which operated between the autumns of 2009 and 2011. In chapter six the objectives, structure and expected outcomes of FND are detailed, and these are used to contextualize the core research problem. With the use of data analysis and fieldwork the thesis seeks to answer whether the national contracted market in labour market attachment has created a more effective and efficient system for transferring the unemployed from benefits into work than the systems before it. Within the broad parameters of the primary question, two further questions are considered. The first, whether the contracting process can identify the best and worst providers in the welfare market, and the second, whether work-first models of welfare-to-work are effective in different economic environments. Using careful data analysis, the results chapter shows that the Flexible New Deal did not meet the government’s own objectives for the programme, and it did not outperform the programmes it was designed to replace. In some areas of the country, the distance from attaining the targets were much greater than others, and these differences are shown to be largely reflective of the labour market characteristics of the operating areas. The thesis concludes by returning to the theme of path dependence established in Chapter 4 as the explanatory factor behind the reform of welfare-to-work programmes. It explains that despite market-driven active labour market policies not meeting their own objectives, the policies are likely to continue to be deployed by future governments.
The FaceBase Consortium: A comprehensive program to facilitate craniofacial research
Creators: name: Visel, Axel
name: Spritz, Richard
name: Dixon, Michael
name: Beaty, Terri H.
name: Donahue, Leah Rae
name: Weinberg, Seth M.
name: Chai, Yang
name: Murray, Stephen
name: Artinger, Kristin
name: Potter, Steven
name: Brinkley, James F.
name: Hallgrimsson, Benedikt
name: Hochheiser, Harry
name: Cunningham, Michael L.
name: Aronow, Bruce J.
name: Klein, Ophir
name: Shapiro, Linda
name: Marazita, Mary L.
name: Clouthier, David
name: Murray, Jeffrey C.
name: Fraser, Scott E.
name: Iwata, Junichi
name: Trainor, Paul A.
name: Postlethwait, John
name: de Villena, Fernando Pardo-Manuel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The FaceBase Consortium consists of ten interlinked research and technology projects whose goal is to generate craniofacial research data and technology for use by the research community through a central data management and integrated bioinformatics hub. Funded by the National Institute of Dental and Craniofacial Research (NIDCR) and currently focused on studying the development of the middle region of the face, the Consortium will produce comprehensive datasets of global gene expression patterns, regulatory elements and sequencing; will generate anatomical and molecular atlases; will provide human normative facial data and other phenotypes; conduct follow up studies of a completed genome-wide association study; generate independent data on the genetics of craniofacial development, build repositories of animal models and of human samples and data for community access and analysis; and will develop software tools and animal models for analyzing and functionally testing and integrating these data. The FaceBase website (http://www.facebase.org) will serve as a web home for these efforts, providing interactive tools for exploring these datasets, together with discussion forums and other services to support and foster collaboration within the craniofacial research community.
title: Structural behaviour of glued laminated timber beams reinforced by compressed wood
Creators: name: Anshari, Buan
Publisher: name: University of Liverpool Repository
Year: 2013

description: As an engineered wood product, glued laminated timber (Glulam) is produced to minimise several natural weaknesses such as knots and non-uniform strength in order to enhance its stiffness and load carrying capacity. Many reinforcement methods have been tested, with promising results in increasing the strength and stiffness of beam. Recently, with increasing concern on environmental protection there is a growing trend in construction to use as many natural materials as possible. Therefore, conventional types of reinforcement using metals and/or synthetic materials do not fit well with this trend. A new approach to strengthen Glulam beams using pure natural materials has been established through this research. Glulam beams were strengthened by inserting compressed wood (CW) blocks into the pre-cut rectangular holes on the top of the beams. This practice was to make use of moisture-dependent swelling nature of the compressed wood. As a result, a pre-camber was produced in the mid-span of the beam reinforced. Significant initial tensile and compressive stresses were generated at both the top and the bottom extreme fibres of the beam, respectively. Material tests have been done to investigate material properties of compressed Japanese cedar with different compression ratios. Structural tests were undertaken for short and long Glulam beams strengthened by CW blocks after gained the pre-camber. 3-D finite element models have also been developed by using commercial code ABAQUS to simulate the pre-stressing behaviour of Glulam beams reinforced using compressed wood blocks. The finite element models were used to simulate the structural behaviour of the pre-stressed beams subjected to subsequent destructive bending tests. All computer models developed were validated against corresponding experimental results of the free moisture-dependent swelling, pre-stressing processes and the destructive tests for both the short and long beams. Reasonably good correlation was obtained in terms of the free swelling, the pre-camber, initial stress state of the Glulam beams reinforced and load-deflection relationships. Using validated computer models, parametric studies were further carried out to provide design information for such a reinforcing technique. The results have indicated that the reinforcing techniques using compressed wood blocks are very effective means to enhance the initial stiffness, bending strength and load carrying capacity of Glulam beams. The technology is ready to be applied in practice.
Ion beam requirements for fast ignition of inertial fusion targets
Creators: name: Honrubia, J. J.
name: Murakami, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: Ion beam requirements for fast ignition are investigated by numerical simulation taking into account new effects such as ion beam divergence not included before. We assume that ions are generated by the TNSA scheme in a curved foil placed inside a re-entrant cone and focused on the cone apex or beyond. From the focusing point to the compressed core ions propagate with a given divergence angle. Ignition energies are obtained for two compressed fuel configurations heated by proton and carbon ion beams. The dependence of the ignition energies on the beam divergence angle and on the position of the ion beam focusing point have been analysed. Comparison between TNSA and quasi-monoenergetic ions is also shown.
description: 11 pages, 10 figures
title: Four-dimensional radiation therapy for thoracic carcinoma : Dosimetric evaluation using deformable image registration
Creators: name: Wong, Victy Yee Wa
Publisher: name: University of Liverpool Repository
Year: 2013

description: Respiratory motion remains a significant challenge for radiation therapy in targeting the tumour. The use of planning margins to avoid geometrical miss of the target volume during respiration results in excessive lung tissue irradiation that limits the prescribed dose to be safely delivered and escalated for better therapeutic gain. The purpose of this study was to develop effective dose planning techniques for treatment to be performed under natural patient breathing. The techniques accounted for the dosimetric influences of tumour movement and aimed to provide an optimized treatment volume by minimizing the internal target volume (ITV) without compromising the target coverage. In the study, the accumulated 4D dose distribution over the tumour volume was calculated using deformable image registration (DIR). A DICOM-RT based tool-box was specially developed for automated 4D dose calculation and evaluations. A new concept of defining the internal target volume from 4D dose coverage, namely inverse ITV (iITV) was introduced via the dose volume enclosed by the minimum accumulated dose in the tumour during the respiratory cycle. The dosimetric advantages of using this iITV with reference to the conventional ITV were confirmed in nine clinical cases by an average dose volume reduction of 16.4% (ranging from 2.3% to 29.9%). 4D radiotherapy involves complex dose distribution which was found to be affected by a number of factors including tumour size, magnitude of tumour displacement, tumour motion characteristics and the reference phases selected for dose planning. Our findings indicate that optimal dose planning was generally, but not always, achieved with the planning CT performed at the temporal mean tumour position and the degree of target coverage maximization strongly depends on the nature of tumour movement. Moreover, the conventionally geometric defined treatment margin could over estimate the treatment volume for a required target coverage. In conclusion, 4D dose calculation based on DIR offers realistic dose estimation, as both geometric and temporal factors are considered, and also provides optimal dose plans by minimizing the treatment volume. However, 4D radiation planning involves a number of factors resulting from the properties of tumours (eg. tumour size, amplitude and characteristics of tumour motion, etc) and from the procedure of treatment planning (eg. reference phase for dose planning, penumbra of dose beam, employed treatment volume etc) that interactively affect the resultant dosimetry. Since these factors vary patient-by-patient, there is no single formula or universal solution that can be used to obtain optimal dose planning. The 4D dose toolbox developed in this study could however provide a user friendly platform for 4D dose calculation and analysis, and allow the optimal treatment modalities and planning techniques to be determined for individuals.
Conditional Aurora A deficiency differentially affects early mouse embryo patterning
Creators: name: Van Dyke, Terry
name: Yoon, Yeonsoo
name: Jones, Stephen N.
name: Cowley, Dale O.
name: Gallant, Judith
name: Rivera-Pérez, Jaime A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Aurora A is a mitotic kinase involved in centrosome maturation, spindle assembly and chromosome segregation during the cell division cycle. In mice, ablation of Aurora A results in mitotic arrest and pre-implantation lethality, preventing studies at later stages of development. Here we report the effects of Aurora A ablation on embryo patterning at early post-implantation stages. Inactivation of Aurora A in the epiblast or visceral endoderm layers of the conceptus leads to apoptosis and inhibition of embryo growth, causing lethality and resorption at approximately E9.5. The effects on embryo patterning, however, depend on the tissue affected by the mutation. Embryos with an epiblast ablation of Aurora A properly establish the anteroposterior axis but fail to progress through gastrulation. In contrast, mutation of Aurora A in the visceral endoderm, leads to posteriorization of the conceptus or failure to elongate the anteroposterior axis. Injection of ES cells into Aurora A epiblast knockout blastocysts reconstitutes embryonic development to E9.5, indicating that the extra-embryonic tissues in these mutant embryos can sustain development to organogenesis stages. Our results reveal new ways to induce apoptosis and to ablate cells in a tissue-specific manner in vivo. Moreover, they show that epiblast-ablated embryos can be used to test the potency of stem cells.
title: Seismotectonics of the southern subduction Chilean margin revealed by recent aftershock sequences
Creators: name: Agurto Detzel, Hans
Publisher: name: University of Liverpool Repository
Year: 2013

description: Subduction margins, as in the case of south-central Chile, are active seismotectonic environments and locus of the world largest earthquakes. In this thesis, two segments of the south-central Chilean subduction margin are studied: (A) the southernmost portion, at the termination of the Nazca-South America convergence (~46ºS), and (B) the segment located between 34º-38ºS, where the Mw 8.8 Maule Earthquake took place in 2010. Analysis of data from a local seismic network deployed in 2004-2005 in area A, indicates low levels of background seismicity with magnitudes ranging 0-3.4 Ml. The seismicity corresponds to shallow crustal events, mostly occurring within the upper 10 km. A third of the seismicity is associated to volcanic activity present in the area, while scarce seismicity is associated with a large strike-slip fault, the Liquiñe-Ofqui Fault System (LOFS), that intersects the region along the arc in a N-S-trend. In 2007, this region was affected by a seismic sequence with a peak of activity associated with a Mw 6.2 earthquake in April that year. A local seismic network was deployed after this main event in order to study its sequence of aftershocks, which provided a unique opportunity to characterise seismotectonically this area that usually lacks intermediate magnitude seismicity, including the calculation of a new local velocity model, accurate aftershock locations and computation of focal mechanisms. The results show P-wave velocities of ~5 km/s for the upper 5 km in accordance with the geology of the area, and low S-wave velocities for the upper 3 km of crust due to rock fracturing and the presence of fluids. An average Vp/Vs ratio of 1.76 was calculated for the region. The alignment of most of the aftershocks within the LOFS plus obtained focal mechanisms, indicate that this sequence had tectonic origin related to the re-activation of the LOFS. Further, a maximum seismogenic depth of about 15 km was determined for the entire region. Regarding area B, affected by a large megathrust earthquake in 2010, the study of moment tensor solutions for the sequence of aftershocks provided new insight into the distribution of postseismic activity relative to co-seismic slip and the release of seismic afterslip. Thrust aftershocks dominate the postseismic activity, but also normal faulting was detected in the outer-rise area and in the overriding plate near the coastline. The largest seismically released afterslip is located between the two main patches of co-seismic slip. Large aftershocks (M>4) occur along the megathrust interface, in zones of intermediate co-seismic slip associated to stress introduced on dislocation tips with high co-seismic slip contrast. On the other hand, smaller events (M
title: The isolation of certain kero bases and a study of their reactions
title: Isolation of certain kerobases and a study of their reactions
titleType: AlternativeTitle
Creators: name: Biggs, Burnard Storey
Publisher: name: The University of Texas at Austin
Year: 1933
Subjects: subject: Kerosene distillate
subject: Kero bases
subject: Kero base isolation
subject: Kero base separation
subject: Kero base analysis
subject: Sulfur dioxide
subject: Kero base reaction
subject: Chemical reagents
subject: Chemical isolation
subject: Substance isolation
subject: Isolation techniques
subject: Reaction mechanisms
subject: Kerosene--Separation
subject: Kerosene--Analysis
subject: Sulfur dioxide
subject: Bases (Chemistry)
subject: Chemical tests and reagents

description: The compounds under investigation in this laboratory at the present time are those basic materials found in the crude kerosene distillate and termed "kerobases". ... The problem ... originally presented was the discovery of some reagent or some process which would be specific for the isolation of an individual substance or some group of substances. ... Sulphur dioxide, while not ideal in many respects, has been found very useful in resolving complex mixtures into more simple mixtures, and ultimately into individual substances. A procedure employing this reagent has been worked out, and by means of it several bases have been obtained in pure form. The succeeding chapters of this paper deal with the technique developed and the compounds isolated, the reactions typical of these and similar bases, and a suggested mechanism explaining these reactions
Underwater Thematic Services Release #2 (U1/U2/U3) software
Creators: name: Campos, Ricard
name: Karantzalos, Konstantinos
Publisher: name: Zenodo
Year: 2021
Subjects: Software
Release
Underwater
Mosaicking
Image Processing
Machine Learning
Bathymetry

description: This deliverable presents the list of the thematic underwater services of WP2 released by NEANIAS project in its second release cycle, due in M23 of the project.
2023-A Prayer for Saint Maron- FINAL.pdf
Creators: name: Hourani, Guita
Publisher: name: figshare
Year: 2023
Subjects: Christian studies
Religion, society and culture
Studies in eastern religious traditions

description: This prayer is part of a Saint Maron Orthodox litany or akathist. A litany is a profound, devotional, highly ornate, poetic hymn of praise that is sung standing. You'll notice as you read or recite this prayer that the anonymous author was well-versed in the saint's life and works. The Romanian litany served as the basis for the English translation.
title: Practice-centred e-health system design for cross-boundary clinical decision support
Creators: name: Anya, Obinna
Publisher: name: University of Liverpool Repository
Year: 2013

description: The idea of cross-boundary clinical decision support has the potential to transform the design of future work environments for e-health through a connected healthcare system that allows for harnessing of information and peer opinion across geographical boundaries for better decision-making. The trouble, however, is that the use of healthcare information in decision-making usually occurs within the context of a complex structure of clinical work practices that is often shaped by a wide range of factors, including organisational culture, local work contexts, socially constructed traditions of actions, experiences and patients’ circumstances. They vary across geographical boundaries, and have remained largely unaccounted for in the design of current e-health systems. As a result, achieving the visions of e-health, particularly in relation to cross-boundary clinical decision support, requires a rethinking of key clinical and organisational processes in a manner that accommodates work practice as a fundamental part of how clinicians work and make decisions in the real-world. This thesis investigates the concept of work practice as a design requirement for cross-boundary clinical decision support systems in e-health. It is argued that the task of enabling informed decision support across geographical boundaries in e-health can be enhanced through an understanding, and a formal characterisation, of work practices in various healthcare work contexts, and a specification of how practice can be used, managed and transformed to suit various clinical problem situations and patients’ needs. This research takes a clinical practice-centred approach to inform e-health system design, and draws on the concept of work practice and cultural-historical theory in social science as well as situation awareness in order to describe the local traditions of actions that guide clinicians’ work in the real world. It contributes a coherent conceptual architecture comprising a practice-centred awareness model for cross-boundary awareness, a frame-based technique, named PracticeFrame, for formalising and representing work practice for system design, and ContextMorph, for adaptively transforming a suggestion across work boundaries to suit a user’s local work context and practices. An in-depth user-informed requirements capture was used to gain an understanding of clinical work practices for designing e-health system for cross-boundary decision support. A proof of concept prototype, named CaDHealth, which is based on the Brahms work practice modelling tool and includes a work practice visualisation model, named the practice display, was developed and used to conduct user-based evaluation. The evaluation revealed that incorporating practice-centred awareness enhances usefulness, acceptance and user adoption of e-health systems for cross-boundary clinical decision support.
Time-resolved lateral spin-caloric transport of optically generated spin packets in n-GaAs
Creators: name: Göbbels, Stefan
name: Güntherodt, Gernot
name: Beschoten, Bernd
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We report on lateral spin-caloric transport (LSCT) of electron spin packets which are optically generated by ps laser pulses in the non-magnetic semiconductor n-GaAs at $T\leq35$K. LSCT is driven by a local temperature gradient induced by an additional cw heating laser. The spatio-temporal evolution of the spin packets is probed using time-resolved Faraday rotation. We demonstrate that the local temperature-gradient induced spin diffusion is solely driven by a non-equilibrium hot spin distribution, i.e. without involvement of phonon drag effects. Additional electric field-driven spin drift experiments are used to verify directly the validity of the non-classical Einstein relation for moderately doped semiconductors at low temperatures for near band-gap excitation.
description: 12 pages, 8 figures
Drosophila melanogaster Zelda and Single-minded collaborate to regulate an evolutionarily dynamic CNS midline cell enhancer
Creators: name: Watson, Joseph D.
name: Crews, Stephen T.
name: Pearson, Joseph C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The Drosophila Zelda transcription factor plays an important role in regulating transcription at the embryonic maternal-to-zygotic transition. However, expression of zelda continues throughout embryogenesis in cells including the developing CNS and trachea, but little is known about its post-blastoderm functions. In this paper, it is shown that zelda directly controls CNS midline and tracheal expression of the link (CG13333) gene, as well as link blastoderm expression. The link gene contains a 5’ enhancer with multiple Zelda TAGteam binding sites that in vivo mutational studies show are required for link transcription. The link enhancer also has a binding site for the Single-minded: Tango and Trachealess:Tango bHLH-PAS proteins that also influences link midline and tracheal expression. These results provide an example of how a transcription factor (Single-minded or Trachealess) can interact with distinct co-regulatory proteins (Zelda or Sox/POU-homeodomain proteins) to control a similar pattern of expression of different target genes in a mechanistically different manner. While zelda and single-minded midline expression is well-conserved in Drosophila, midline expression of link is not well-conserved. Phylogenetic analysis of link expression suggests that ~60 million years ago, midline expression was nearly or completely absent, and first appeared in the melanogaster group (including D. melanogaster, D. yakuba, and D. erecta) >13 million years ago. The differences in expression are due, in part, to sequence polymorphisms in the link enhancer and likely due to altered binding of multiple transcription factors. Less than 6 million years ago, a second change occurred that resulted in high levels of expression in D. melanogaster. This change may be due to alterations in a putative Zelda binding site. Within the CNS, the zelda gene is alternatively spliced beginning at mid-embryogenesis into transcripts that encode a Zelda isoform missing three zinc fingers from the DNA binding domain. This may result in a protein with altered, possibly non-functional, DNA-binding properties. In summary, Zelda collaborates with bHLH-PAS proteins to directly regulate midline and tracheal expression of an evolutionary dynamic enhancer in the post-blastoderm embryo.
On Discovering Co-Location Patterns in Datasets: A Case Study of Pollutants and Child Cancers
Creators: name: Li, Jundong
name: Adilmagambetovm, Aibek
name: Jabbar, Mohomed Shazan Mohomed
name: Zaiane, Osmar R.
name: Osornio-Vargas, Alvaro
name: Wine, Osnat
Publisher: name: arXiv
Year: 2014
Subjects: subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: We intend to identify relationships between cancer cases and pollutant emissions and attempt to understand whether cancer in children is typically located together with some specific chemical combinations or is independent. Co-location pattern analysis seems to be the appropriate investigation to perform. Co-location mining is one of the tasks of spatial data mining which focuses on the detection of co-location patterns, the sets of spatial features frequently located in close proximity of each other. Most previous works are based on transaction-free apriori-like algorithms which are dependent on user-defined thresholds and are designed for boolean data points. Due to the absence of a clear notion of transactions, it is nontrivial to use association rule mining techniques to tackle the co-location mining problem. The approach we propose is based on a grid "transactionization" of the geographic space and is designed to mine datasets with extended spatial objects. Uncertainty of the feature presence in transactions is taken into account in our model. The statistical test is used instead of global thresholds to detect significant co-location patterns and rules. We evaluate our approach on synthetic and real datasets. This approach can be used by researchers looking for spatial associations between environmental and health factors. In addition, we explain the data modelling framework which is used on real datasets of pollutants (PRTR/NPRI) and childhood cancer cases.
description: In GeoInformatica, 2016
Leucine and arginine regulate trophoblast motility through mTOR-dependent and independent pathways in the preimplantation mouse embryo
Creators: name: Martin, Patrick M.
name: Sutherland, Ann E.
name: Mager, Sela
name: González, Isabel M.
name: Sloan, Jennifer L.
name: Harris, Thurl
name: Burdsal, Carol
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Uterine implantation is a critical element of mammalian reproduction and is a tightly and highly coordinated event. An intricate and reciprocal uterine-embryo dialog exists to synchronize uterine receptivity with the concomitant activation of the blastocyst, maximizing implantation success. While a number of pathways involved in regulating uterine receptivity have been identified in the mouse, less is understood about blastocyst activation, the process by which the trophectoderm (TE) receives extrinsic cues that initiate new characteristics essential for implantation. Amino acids (AA) have been found to regulate blastocyst activation and TE motility . In particular, we find that arginine and leucine alone are necessary and sufficient to induce TE motility. Both arginine and leucine act individually and additively to propagate signals that are dependent on the activity of the mammalian target of rapamycin complex 1 (mTORC1). The activities of the well-established downstream targets of mTORC1, p70S6K and 4EBP, do not correlate with trophoblast motility, suggesting that an independent-rapamycin-sensitive pathway operates to induce trophoblast motility, or that other, parallel amino acid-dependent pathways are also involved. We find that endogenous uterine factors act to induce mTORC1 activation and trophoblast motility at a specific time during pregnancy, and that this uterine signal is later than the previously defined signal that induces the attachment reaction. matured blastocysts exhibit competence to respond to an 8-hour AA stimulus by activating mTOR and subsequently undergoing trophoblast outgrowth by the morning of day 4.5 of pregnancy, but not on day 3.5. By the late afternoon of day 4.5, the embryos no longer require any exposure to AA to undergo trophoblast outgrowth , demonstrating the existence and timing of an equivalent signal. These results suggest that there are two separate uterine signals regulating implantation, one that primes the embryo for the attachment reaction and another that activates mTOR and initiates invasive behavior.► Arginine and leucine are necessary and sufficient to induce trophoblast motility. ► Arginine and leucine have both mTORC1-dependent and independent actions. ► p70S6K or 4EBP activity do not correlate with motility suggesting a separate pathway. ► mTOR activation suggests uterine factors induce mTORC1 regulated motility. ► Amino acids may be components of the uterine-embryo implantation crosstalk.
Time-lapse imaging reveals stereotypical patterns of Drosophila midline glial migration
Creators: name: Wheeler, Scott R.
name: Pearson, Joseph C.
name: Crews, Stephen T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The Drosophila CNS midline glia (MG) are multifunctional cells that ensheath and provide trophic support to commissural axons, and direct embryonic development by employing a variety of signaling molecules. These glia consist of two functionally distinct populations: the anterior MG (AMG) and posterior MG (PMG). Only the AMG ensheath axon commissures, whereas the function of the non-ensheathing PMG is unknown. The Drosophila MG have proven to be an excellent system for studying glial proliferation, cell fate, apoptosis, and axon-glial interactions. However, insight into how AMG migrate and acquire their specific positions within the axon-glial scaffold has been lacking. In this paper, we use time-lapse imaging, single-cell analysis, and embryo staining to comprehensively describe the proliferation, migration, and apoptosis of the Drosophila MG. We identified 3 groups of MG that differed in the trajectories of their initial inward migration: AMG that migrate inward and to the anterior before undergoing apoptosis, AMG that migrate inward and to the posterior to ensheath commissural axons, and PMG that migrate inward and to the anterior to contact the commissural axons before undergoing apoptosis. In a second phase of their migration, the surviving AMG stereotypically migrated posteriorly to specific positions surrounding the commissures, and their final position was correlated with their location prior to migration. Most noteworthy are AMG that migrated between the commissures from a ventral to a dorsal position. Single-cell analysis indicated that individual AMG possessed wide-ranging and elaborate membrane extensions that partially ensheathed both commissures. These results provide a strong foundation for future genetic experiments to identify mutants affecting MG development, particularly in guidance cues that may direct migration. Drosophila MG are homologous in structure and function to the glial-like cells that populate the vertebrate CNS floorplate, and study of Drosophila MG will provide useful insights into floorplate development and function.
title: Technological change or consistency? an investigation of faience produced from the Middle to the New Kingdom at Abydos, Egypt.
Creators: name: Hammerle, Esme
Publisher: name: University of Liverpool Repository
Year: 2013

description: For many years, it has been argued that faience underwent dramatic technological changes from the Middle Kingdom (2040–1640 BC) to the New Kingdom (1570–1070 BC) in Egypt. These technological developments are said to include changes in the sources of some of the key ingredients of faience production, including the silica, alkali, and colourant. However, the proposed technological changes are broad generalizations and, in the case of some faience bead assemblages, they appear to be non-existent. This thesis considers the reasons for the developments in faience production, and focuses on the changes themselves by analysing the chemical composition of faience beads from the Middle to the New Kingdom at the site of Abydos. This research focuses on a sample of 151 beads, dating from the Middle Kingdom to the New Kingdom, which were found during John Garstang’s early 20th Century excavations. All aspects of the beads were investigated in order to establish the production methods used – this was, in essence, reverse engineering of the beads. The investigation was accomplished with a combination of established and innovative analytical methods, some of which had not been tested on faience material before. Scanning electron microscopy (SEM) was employed to determine changes in the microstructure, and led to an understanding of the glazing methods used in the production of the beads. Energy dispersive spectrometry (EDS) was used to test the chemical composition of the samples. Strontium isotope analysis was conducted to identify the raw material sources of the alkali used in the production of the beads. Electron backscatter diffraction (EBSD) was undertaken to determine the firing temperatures reached during production, and crystallography (CL) was undertaken to determine the silica source. Once these analyses were complete the archaeological samples were experimentally replicated and analysed. All of the results were then interrogated in order to prove, scientifically, whether or not Egyptian faience technology really underwent change from one period to the next.
Fluctuation spectra of weakly driven nonlinear systems
Creators: name: Zhang, Yaxing
name: Tadokoro, Yukihiro
name: Dykman, M. I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We show that in periodically driven systems, along with the delta-peak at the driving frequency, the spectral density of fluctuations displays extra features. These can be peaks or dips with height quadratic in the driving amplitude, for weak driving. For systems where inertial effects can be disregarded, the peaks/dips are generally located at zero frequency and at the driving frequency. The shape and intensity of the spectra very sensitively depend on the parameters of the system dynamics. To illustrate this sensitivity and the generality of the effect, we study three types of systems: an overdamped Brownian particle (e.g., an optically trapped particle), a two-state system that switches between the states at random, and a noisy threshold detector. The analytical results are in excellent agreement with numerical simulations.
Computational insight of antioxidant and doxorubicin combination for effective cancer therapy
Creators: name: Nayak, Jyotsnamayee
name: P., Seshu Vardhan
name: Sahoo, Suban K.
name: Kumar, Manish
name: Vashistha, Vinod Kumar
name: Kumar, Rajender
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Medicine
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer
Plasma Physics

description: Doxorubicin (DOX) is the most effective antineoplastic agent, destroys cancer cells by interrupting cellular function. However, the serious side effects on the heart limits its utility. To curb these unwanted side effects, nutritionist recommend antioxidants use along with DOX while chemotherapy. But it was not supported by various oncologists as it can alter the toxicity of DOX towards cancer cells. Therefore, here we explored the in silico pharmacokinetics and combination effect of DOX and antioxidants on topoisomerases-II (Top-II) and cyclophilin D (Cyp-D) therapeutic targets involved in cancer proliferation and post-myocardial infarction, respectively. The molecular docking study was conducted on target proteins and DOX including most prescribed antioxidants (melatonin, N-acetylcysteine (NAC), glutathione (GSH), β-carotene and vitamin C). GSH showed effective binding potential for Top-II and Cyp-D active sites, but other considered antioxidants possess low binding affinity. The highest docked conformations were subjected to molecular dynamics (MD) simulations to understand conformer stability of DOX and GSH with Cyp-D and Top-II for 100 ns. The results revealed that ligands pose at Top-II active sites where DOX showed strong binding affinity to DNA binding pocket and GSH to a buried site. The computational data summarised and proposed the GSH and DOX combination as antagonist effects on Top-II. Conversely, the binding compactness of GSH improved due to surface fit at the active pocket of Cyp-D and completely blocking DOX binding affinity, suppress adverse reactions of post-myocardial infarction. Communicated by Ramaswamy H. Sarma
BMPER-induced BMP signaling promotes coronary artery remodeling
Creators: name: Moser, Martin
name: Dyer, Laura
name: Patterson, Cam
name: Wu, Yaxu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The connection of the coronary vasculature to the aorta is one of the last essential steps of cardiac development. However, little is known about the signaling events that promote normal coronary artery formation. The bone morphogenetic protein (BMP) signaling pathway regulates multiple aspects of endothelial cell biology but has not been specifically implicated in coronary vascular development. BMP signaling is tightly regulated by numerous factors, including BMP-binding endothelial cell precursor-derived regulator (BMPER), which can both promote and repress BMP signaling activity. In the embryonic heart, BMPER expression is limited to the endothelial cells and the endothelial-derived cushions, suggesting that BMPER may play a role in coronary vascular development. Histological analysis of BMPER−/− embryos at early embryonic stages demonstrates that commencement of coronary plexus differentiation is normal and that endothelial apoptosis and cell proliferation are unaffected in BMPER−/− embryos compared with wild-type embryos. However, analysis between embryonic days 15.5-17.5 reveals that, in BMPER−/− embryos, coronary arteries are either atretic or connected distal to the semilunar valves. In vitro tubulogenesis assays indicate that isolated BMPER−/− endothelial cells have impaired tube formation and migratory ability compared with wild-type endothelial cells, suggesting that these defects may lead to the observed coronary artery anomalies seen in BMPER−/− embryos. Additionally, recombinant BMPER promotes wild-type ventricular endothelial migration in a dose-dependent manner, with a low concentration promoting and high concentrations inhibiting migration. Together, these results indicate that BMPER-regulated BMP signaling is critical for coronary plexus remodeling and normal coronary artery development.
Inklusion und Volksschule. Ein Erfolgsmodell? Eine empirische Analyse im Kanton Zürich zum Vergleich von drei Inklusionsmodellen
Creators: name: Stark, Isabell
Publisher: name: Zenodo
Year: 2023
Subjects: Sonderpädagogik
Masterarbeit
Inklusion
Volksschule
Inklusionsmodelle
Kanton Zürich

description: Mit der vorliegenden Masterarbeit wird das aktuelle und rege diskutierte Thema Inklusion an den Volksschulen aufgenommen. Insbesondere wird der Fokus auf die vorhandenen Inklusionsmodelle gerichtet. In der Praxis sind einige Modelle vorhanden. Doch welche tragen zur Inklusion bei? Und wie werden aktuelle Inklusionsmodelle unter Berücksichtigung von Schülerinnen und Schülern mit Risiken in der sozio-emotionalen Entwicklung umgesetzt? Um die Forschungsfragen zu beantworten, wurden drei Modelle aus dem Kanton Zürich analysiert und miteinander verglichen. Die Analyse beruht auf fünf Expertinnen- und Experteninterviews und zeigt, dass alle drei Modelle unterschiedliche Beiträge zur Integration von Schülerinnen und Schülern mit besonderen pädagogischen Bedürfnissen leisten können.