cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Supplementary documentation for SAEON's field instrument data collected at the Cathedral Peak CAT3 #1 station
Creators: name: South African Environmental Observation Network (SAEON) Grasslands-Forests-Wetlands Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Cathedral Peak
Hydrological
Soil Diviner tube
Soil water content

description: This package contains supporting information for the hydrological data collected at Cathedral Peak's CAT3 #1 station, as part of the South African Environmental Observation Network's monitoring projects.
Ubaldino Peruzzi a … (29 gennaio 1871)
Creators: name: Peruzzi, Ubaldino
Publisher: name: Zenodo
Year: 2023
Subjects: Accademia dei Georgofili
Peruzzi, Ubaldino
Carteggio
Lettera
Letter
Correspondence
1871

description: Lettera di Ubaldino Peruzzi a ... del 29 gennaio 1871. Segnatura dell’unità documentale: Archivio storico dell’Accademia dei Georgofili, Carteggio, Busta 36, 4588. Natura: manoscritto. Consistenza: cc. 2
description: Digitalizzato come parte della Mostra virtuale: Ubaldino Peruzzi : un percorso in rete : in occasione del bicentenario della nascita https://www.georgofili.it/contenuti/ubaldino-peruzzi-un-percorso-in-rete/17485
A splicing isoform of TEAD4 attenuates the Hippo–YAP signalling to inhibit tumour proliferation
Creators: name: Zhao, Jinyao
name: Wang, Yang
name: Qian, Haili
name: Liu, Quentin
name: Wei, Huanhuan
name: Wang, Zefeng
name: Zhang, Wenjing
name: Fan, Xiaojuan
name: Yu, Jing
name: Tsai, Yi-Hsuan S.
name: Meng, Songshu
name: Qi, Yangfan
name: Han, Wei
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Aberrant splicing is frequently found in cancer, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo–YAP signalling, a key pathway that regulates cell proliferation and organ size, is under control of a splicing switch. We show that TEAD4, the transcription factor that mediates Hippo–YAP signalling, undergoes alternative splicing facilitated by the tumour suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks an N-terminal DNA-binding domain, but maintains YAP interaction domain. TEAD4-S is located in both the nucleus and cytoplasm, acting as a dominant negative isoform to YAP activity. Consistently, TEAD4-S is reduced in cancer cells, and its re-expression suppresses cancer cell proliferation and migration, inhibiting tumour growth in xenograft mouse models. Furthermore, TEAD4-S is reduced in human cancers, and patients with elevated TEAD4-S levels have improved survival. Altogether, these data reveal a splicing switch that serves to fine tune the Hippo–YAP pathway.
AKAP95 regulates splicing through scaffolding RNAs and RNA processing factors
Creators: name: Wang, Zefeng
name: Shah, Kushani
name: Jiang, Hao
name: Yang, Zhenhua
name: Mao, Miaowei
name: Hu, Jing
name: Khodadadi-Jamayran, Alireza
name: Nasim, Md Talat
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95, has a remarkable activity in enhancing chromatin transcription. In this study, we show that AKAP95 interacts with many factors involved in transcription and RNA processing, including selective groups of hnRNP proteins, through its N-terminal region, and directly regulates pre-mRNA splicing. AKAP95 binds preferentially to proximal intronic regions on pre-mRNAs in human transcriptome, and this binding requires its zinc-finger domains. By selectively coordinating with hnRNP H/F and U proteins, AKAP95 appears to mainly promote the inclusion of many exons in the genome. AKAP95 also directly interacts with itself. Taken together, our results establish AKAP95 as a mostly positive regulator of pre-mRNA splicing and a possible integrator of transcription and splicing regulation.
title: The impact of soil-transmitted helminth and respiratory viral infections on Streptococcus pneumoniae nasopharyngeal carriage
Creators: name: Law, Alice
Publisher: name: University of Liverpool Repository
Year: 2020

description: The burden of invasive disease caused by S. pneumoniae is greatest in resource-constrained, low-income regions of the world where soil-transmitted helminth (STH) and respiratory viral infections are also highly prevalent. Research has indicated an ability of STHs and respiratory viral infections to worsen pneumococcal disease, however our understanding of the effect of these co-infecting pathogens on the immunological mechanisms that govern pneumococcal colonisation, a prerequisite for invasive disease development, is limited. Hence, the potential of concurrent STH and respiratory virus infection to alter host immune responses crucial to the control of S. pneumoniae nasopharyngeal carriage was investigated, using a combination of mouse models, in vitro assays and human studies based in low-income settings. This thesis presents the first measure of pneumococcal and STH co-infection in a field-setting, providing baseline data on pneumococcal carriage prevalence and density in children with simultaneous helminth infection. Concurrent STH infection was associated with increased pneumococcal carriage density amongst a cohort of children in Ecuador, supporting observations, made in this thesis, of high-density colonisation in mice co-infected with the murine whipworm, T. muris. Increased colonisation densities, alongside high carriage prevalence rates, were also evident in individuals with concurrent respiratory virus infection in a second clinical study, conducted in Malawi. For both STH and respiratory viral co-infection, an enhanced inflammatory phenotype was linked to high-density colonisation, characterised by elevated pro-inflammatory cytokine production and muted tolerogenic responses. Together, data here suggest that the epidemiology of pneumococcal carriage and disease may be influenced by widespread co-infection with respiratory viruses and STHs, providing insight into the differences in pneumococcal dynamics between high and low-income countries. The ability of co-infection to disrupt the balance between tolerogenic and inflammatory responses that govern pneumococcal carriage was highlighted, opening exciting avenues for interventions that target the co-infecting pathogen and/or the consequential immune skew, to aid in the control and prevention of pneumococcal disease.
Critical Scaling of Bagnold Rheology at the Jamming Transition of Frictionless Two Dimensional Disks
Creators: name: Vagberg, Daniel
name: Olsson, Peter
name: Teitel, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: FOS: Physical sciences

description: We carry out constant volume simulations of steady-state, shear driven, rheology in a simple model of bidisperse, soft-core, frictionless disks in two dimensions, using a dissipation law that gives rise to Bagnoldian rheology. We carry out a detailed critical scaling analysis of our resulting data for pressure $p$ and shear stress $σ$, in order to determine the critical exponent $β$ that describes the algebraic divergence of the Bagnold transport coefficients, as the jamming transition is approached from below. We show that it is necessary, for the strain rates considered in this work, to consider the leading correction-to-scaling term in order to achieve a self-consistent analysis of our data. Our resulting value $β\approx 5.0\pm 0.4$ is clearly larger than the theoretical prediction by Otsuki and Hayakawa, and is consistent with earlier numerical results by Peyneau and Roux, and recent theoretical predictions by DeGiuli et al. We have also considered the macroscopic friction $μ\equiv σ/p$ and similarly find results consistent with Peyneau and Roux, and with DeGiuli et al. Our results confirm that the shear driven jamming transition in Bagnoldian systems is well described by a critical scaling theory (as was found previously for Newtonian systems), and we relate this scaling theory to the phenomenological constituent laws for dilatancy and friction.
description: 20 pages, 21 figures; revised manuscript according to published version
Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism
Creators: name: Ding, Jin-Dong
name: Jiang, Yong-Hui
name: Xu, Qiong
name: Hayrapetyan, Volodya
name: Gaidis, Erin
name: Zhao, Shengli
name: Weinberg, Richard J.
name: Dutta, Nisha
name: Yin, Henry
name: Duffney, Lara J.
name: Hulbert, Samuel W.
name: Chung, Leeyup
name: Wang, Fan
name: Badea, Alexandra
name: Kim, Namsoo
name: Bey, Alexandra L.
name: Kumar, Sunil
name: Dzirasa, Kafui
name: David, Lisa K.
name: Wang, Xiaoming
name: Rodriguiz, Ramona M.
name: Mague, Stephen D.
name: Katz, Brittany M.
name: Wetsel, William C.
name: Yu, Chunxiu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Human neuroimaging studies suggest that aberrant neural connectivity underlies behavioural deficits in autism spectrum disorders (ASDs), but the molecular and neural circuit mechanisms underlying ASDs remain elusive. Here, we describe a complete knockout mouse model of the autism-associated Shank3 gene, with a deletion of exons 4–22 (Δe4–22). Both mGluR5-Homer scaffolds and mGluR5-mediated signalling are selectively altered in striatal neurons. These changes are associated with perturbed function at striatal synapses, abnormal brain morphology, aberrant structural connectivity and ASD-like behaviour. In vivo recording reveals that the cortico-striatal-thalamic circuit is tonically hyperactive in mutants, but becomes hypoactive during social behaviour. Manipulation of mGluR5 activity attenuates excessive grooming and instrumental learning differentially, and rescues impaired striatal synaptic plasticity in Δe4–22−/− mice. These findings show that deficiency of Shank3 can impair mGluR5-Homer scaffolding, resulting in cortico-striatal circuit abnormalities that underlie deficits in learning and ASD-like behaviours. These data suggest causal links between genetic, molecular, and circuit mechanisms underlying the pathophysiology of ASDs.
title: 'Other Children, Other Voices': Education and Exclusion and the Duty to 'Progressively Realize' Children's Rights
Creators: name: Byrne, Seamus
Publisher: name: University of Liverpool Repository
Year: 2023

description: Children’s socio-economic rights are once again at the centre of international legal and developmental discourses. With the memory and impact of the global economic crisis still an unforgiving reality for many children, in addition to the abundance of evidence confirming that children’s access to and enjoyment of their socio-economic rights have been seriously impaired, this thesis examines the very foundations upon which those rights are legally constructed. By unpacking the principle of progressive realization which underpins the delivery and realization of all socio-economic rights, this thesis argues that it can become a more durable and persuasive concept within children’s human rights law to guide and consolidate state practice regarding the fulfillment of their socio-economic rights commitments. To frame the analysis, this thesis invokes the right to education and specifically the phenomenon of school exclusions to demonstrate how progressive realization can become much more than an abstracted legal concept but rather a robust and influential tool to further enhance children’s socio-economic rights. By adopting a child-participatory methodology to investigate school exclusions in England, this thesis tests the legal framework which governs exclusion and examines whether it is consistent with the obligation of the state to progressively realize children’s rights. This thesis concludes by highlighting a number of deficiencies within the school exclusion system in England which run counter to the very notion of progressively realizing children’s rights. From the absence of information, to the lack of accountability and the failure to consider and apply fundamental children’s rights standards such as the right to be heard and the child’s best interests principle, this thesis exposes a number of areas where children’s rights are found wanting. To respond to this, and to give effect to the principle of progressive realization, this thesis concludes by advancing a number of recommendations across two distinct fronts. The first set of recommendations proposes how children’s rights scholarship as a whole can better re-engage and embrace the principle of progressive realization so that it can have a reformist legacy within children rights and human rights law more broadly. Central to this is the proposal that the Committee on the Rights of the Child promulgate a new General Comment on Progressive Realization. Following on from this, a number of recommendations are subsequently advanced as to how the school exclusion system in England itself can be remedied to better comply with the principle of progressive realization.
Maxwell's Optics Symplectic Hamiltonian
Creators: name: Kulyabov, D. S.
name: Korolkova, A. V.
name: Sevastyanov, L. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The Hamiltonian formalism is extremely elegant and convenient to mechanics problems. However, its application to the classical field theories is a difficult task. In fact, you can set one to one correspondence between the Lagrangian and Hamiltonian in the case of hyperregular Lagrangian. It is impossible to do the same in gauge-invariant field theories. In the case of irregular Lagrangian the Dirac Hamiltonian formalism with constraints is usually used, and this leads to a number of certain difficulties. The paper proposes a reformulation of the problem to the case of a field without sources. This allows to use a symplectic Hamiltonian formalism. The proposed formalism will be used by the authors in the future to justify the methods of vector bundles (Hamiltonian bundles) in transformation optics.
description: in Russian, in English
Spin-orbit coupling and chaotic rotation for circumbinary bodies. Application to the small satellites of the Pluto-Charon system
Creators: name: Correia, Alexandre C. M.
name: Leleu, Adrien
name: Rambaux, Nicolas
name: Robutel, Philippe
Publisher: name: arXiv
Year: 2015
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Chaotic Dynamics (nlin.CD)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: We investigate the resonant rotation of circumbinary bodies in planar quasi-circular orbits. Denoting $n_b$ and $n$ the orbital mean motion of the inner binary and of the circumbinary body, respectively, we show that spin-orbit resonances exist at the frequencies $n\pm kν/2$, where $ν= n_b - n$, and $k$ is an integer. Moreover, when the libration at natural frequency has the same magnitude as $ν$, the resonances overlap and the rotation becomes chaotic. We apply these results to the small satellites in the Pluto-Charon system, and conclude that their rotations are likely chaotic. However, the rotation can also be stable and not synchronous for small axial asymmetries.
description: 7 pages, 4 figures
DCAF1 controls T-cell function via p53-dependent and -independent mechanisms
Creators: name: Zou, Liyun
name: Guo, Zengli
name: Liu, Cui
name: Xiong, Yue
name: Wan, Yisong Y.
name: Zhang, Song
name: Whitmire, Jason K.
name: Kong, Qing
name: Yan, Feng
name: Chen, Xian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: On activation, naive T cells grow in size and enter cell cycle to mount immune response. How the fundamental processes of T-cell growth and cell cycle entry are regulated is poorly understood. Here we report that DCAF1 (Ddb1–cullin4-associated-factor 1) is essential for these processes. The deletion of DCAF1 in T cells impairs their peripheral homeostasis. DCAF1 is upregulated on T-cell receptor activation and critical for activation-induced T-cell growth, cell cycle entry and proliferation. In addition, DCAF1 is required for T-cell expansion and function during anti-viral and autoimmune responses in vivo. DCAF1 deletion leads to a drastic stabilization of p53 protein, which can be attributed to a requirement of DCAF1 for MDM2-mediated p53 poly-ubiquitination. Importantly, p53 deletion rescues the cell cycle entry defect but not the growth defect of DCAF1-deficient cells. Therefore, DCAF1 is vital for T-cell function through p53-dependent and -independent mechanisms.
title: DESIGNING A HUMAN CELL PERFUSION BIOREACTOR SYSTEMS UTILISING BIOMATERIALS TO ENRICH STEM CELL NICHES FOR THE RED BLOOD CELLS PRODUCTION
Creators: name: Bin Rahmat Sam, Mohd Fuad
Publisher: name: University of Liverpool Repository
Year: 2024

description: The short shelf life along with the constant threat or an actual shortage of red blood cells (RBCs) places an ever-present constant stress on the healthcare providers to maintain and then increase blood donations to meet blood product demands. Blood transfusion services are already at a critical point trying to meet this constant and increasing demand. Made worse by the low numbers of people actually donating blood (7% U.K., 13% Taiwan). To add to this time dependant critical balance for blood supply and demand, the increase in outbreaks in the transmission of blood carried infectious diseases have caused safety issues. For many years, a number of researchers around the world have been attempting to use progenitor cells from various sources as the origin to produce RBCs; these include bone marrow, umbilical cord blood and mobilised peripheral blood. In order to avoid any potential negative side effects associated with stem cell-mobilizing agents, the research in this thesis utilised steady state peripheral blood as the potential source for in vitro RBC production.
Dimensions of the Post-Internet Condition. An Exploration through Post-Internet Art
Creators: name: Christou, Elisavet
Publisher: name: Lancaster University
Year: 2022
Subjects: port-Internet
post-Internet art
Internet research
rhizomatic
digital art
mediation
appropriation
identity
publics
public sphere
spatiotemporality

description: This thesis introduces post-Internet art as a novel exploratory medium for Internet research. The thesis proposes that post-Internet art as a cultural product of information and communication technologies (ICTs) can operate as an investigating mechanism of the post-Internet condition. Through a rhizomatic methodological approach and the application of a sociotechnical and a technocultural lens, the research work examines post-Internet art’s rhizomatic unity to the world. Post-internet art reflects the developments in ICTs and the World Wide Web approximately from 2005 to 2020, like ubiquitous computing and semantic web. The thesis examines a large number of post-Internet artworks and makes connections to discourse from Internet-related research fields like media theory, digital cultures and digital humanities. Five key dimensions of the post-Internet condition are identified; these are appropriation, mediation, spatiotemporality, publics and public spheres, and identity. The concept of dimensions is used to discuss the ways of considering the post-Internet condition. These ways are analysed as interconnected elements that make up a whole within a historical present. The findings offer a new expanded view into how we can better define and understand our contemporary condition through the medium of post-Internet art. The artworks examined in this thesis include works by artists: Oliver Laric, Jennifer Chan, Krystal South, Jon Rafman, Erica Scourti, Evan Roth, James Bridle, Heath Bunting, Benjamin Grosser, Jay Simons, Guido Segni, Zach Blas, Jonas Lund, Filippo Minelli, Cuadalupe Rosales, Natalie Bookchin, Amalia Ulman, Jeremy Bailey, Ed Fornieles, Bogosi Sekhukhuni and Jake Elwes.
Mapping Starspots on AU Mic to Complement Hubble Transmission Spectrum Observations of AU Mic b
Creators: name: Waalkes, William
name: Berta-Thompson, Zachory
name: Newton, Elisabeth
name: Mann, Andrew
name: Gao, Peter
name: Wakeford, Hannah
name: Alderson, Lili
Publisher: name: Zenodo
Year: 2023
Subjects: Exoplanets
AU Mic
Starspots
TLSE
Transits
Spectrophotometry

description: AU Mic is a 30 Myr pre-main sequence M dwarf in the stellar neighborhood (d=9.7 pc) which is very active and has a rotation period of 4.86 days. There are at least two known planets orbiting AU Mic, AU Mic b and c are both warm Neptunes (R$_{p,b}$ = 4.1 \Rearth and R$_{p,bc}$ = 3.2 \Rearth) on 8.46 and 18.86-day periods, respectively. AU Mic has a heavily spotted surface as evidenced in its strong photometric rotational modulations. The transmission spectrum of AU Mic b is being observed with Hubble, and we aim to better understand unocculted starspots using ground-based photometry and spectra in order to complement those observations and better constrain the planetary transmission spectrum. Unocculted spots can introduce spurious transit depth variations seen in transmission spectra, known as the Transit Light Source Effect (TLSE). Unocculted spots affect not only the in-transit interpretation of transmission spectra, but also the out-of-transit temporal and wavelength variations in the stellar flux. By studying the stellar spectrum out of transit, we may be able to independently constrain the spectral signatures of AU Mic’s starspots so we can correct their effect in the atmospheric observations of the planet. We gathered LCO 0.4m SBIG photometry in broad bandpasses to study the star’s rotational modulations and LCO NRES high-resolution spectra to model the effect of multiple spectral components on the integrated spectrum of the star. To model the combination of contemporaneous photometric and spectroscopic observations taken by different ground based observatories, we built a self-consistent statistical inference framework which jointly models the multi-color photometric variability and normalized high-resolution spectra parameterized by spot coverage fraction and temperature. Applied across multiple NRES spectral orders, this method generates precise constraints on spot characteristics which are then used to forward-model the spot contamination spectrum.
description: {"references": ["Gilbert, E. et al. (2022), AJ, 163, 147G", "Husser, T. et al. (2013), A&A, 553A, 6H", "Libby-Roberts, J. et al. (2022), AJ, 164, 59L", "Plavchan, P. et al. (2020), Nature, 582, 497P", "Rackham, B. et al. (2018), ApJ, 853, 122R"]}
Exploring student difficulties with observation location
Creators: name: Bryant, Jaime
name: Dawod, Rita
name: Fischer, Susan M.
name: Kustusch, Mary Bridget
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics Education (physics.ed-ph)
subject: FOS: Physical sciences

description: Throughout introductory physics, students create and interpret free body diagrams in which multiple forces act on an object, typically at a single location (the object's center of mass). The situation increases in difficulty when multiple objects are involved, and further when electric and magnetic fields are present. In the latter, sources of the fields are often identified as a set of electric charges or current-carrying wires, and students are asked to determine the electric or magnetic field at a separate location defined as the observation location. Previous research suggests students struggle with accounting for how a measurement or calculation depends on the observation location. We present preliminary results from a studio-style, algebra-based, introductory electricity and magnetism course showing the prevalence of correct and incorrect responses to questions about observation location by analyzing student written work involving vector addition of fields.
Exploring how care home staff manage responsive behaviours, associated with dementia, in care homes in Ireland, during the Covid-19 pandemic
Creators: name: O'Donnell, Elizabeth
Publisher: name: Lancaster University
Year: 2022
Subjects: care homes
Dementia
responsiveness • psychotropic medication
person-centred care

description: Introduction: Care home residents with dementia often exhibit responsive behaviours including agitation, aggression and wandering. Psychotropic drugs are often prescribed to manage responsive behaviours but contravene guidance as they increase the risk of serious adverse events and death in people with dementia. Aim: This thesis aims to understand how care home staff manage responsive behaviours to identify the barriers and facilitators to implementing a non-pharmacological approach to behaviour management. Methods: This thesis was underpinned by the transformative paradigm and critical theory. A review of qualitative studies was conducted to synthesise understanding of the facilitators or barriers to implementing non-pharmacological strategies to behaviour management (PROSPERO protocol registration CRD42020165948). The findings from the review, in addition to a qualitative survey and patient and public Involvement informed the design of the qualitative interview study to understand how responsive behaviours are managed by care home staff in the Republic of Ireland (ROI) prior to, and during the Covid-19 pandemic. In total, 25 interviews were conducted with staff from 21 care homes across Ireland. Reflexive thematic analysis of qualitative data was informed by Braun and Clarke (2019). All participants provided written informed consent. Ethical approval was obtained from Lancaster University. Findings: The findings from the systematic review and qualitative study found the barriers to taking a non-pharmacological approach to manage responsive behaviours included inadequate staff training and multidisciplinary collaboration. The qualitative study extends current knowledge by showing that a power hierarchy exists between healthcare assistants and nurses that posed a barrier to taking a non-pharmacological approach to behaviour management. Facilitators to taking a non-pharmacological approach included effective leadership and family involvement in resident care. Conclusion: This thesis extends knowledge by conceptualising how responsive behaviours are managed using both pharmacological and non-pharmacological approaches to identify the facilitators and barriers to implementing non-pharmacological strategies to behaviour management.
Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
Creators: name: Lundberg, Derek S.
name: Dangl, Jeffery L.
name: Del Rio, Tijana G.
name: Wagner, Maggie R.
name: Mitchell-Olds, Thomas
name: Tringe, Susannah G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
Causal Decision Trees
Creators: name: Li, Jiuyong
name: Ma, Saisai
name: Le, Thuc Duy
name: Liu, Lin
name: Liu, Jixue
Publisher: name: arXiv
Year: 2015
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Uncovering causal relationships in data is a major objective of data analytics. Causal relationships are normally discovered with designed experiments, e.g. randomised controlled trials, which, however are expensive or infeasible to be conducted in many cases. Causal relationships can also be found using some well designed observational studies, but they require domain experts' knowledge and the process is normally time consuming. Hence there is a need for scalable and automated methods for causal relationship exploration in data. Classification methods are fast and they could be practical substitutes for finding causal signals in data. However, classification methods are not designed for causal discovery and a classification method may find false causal signals and miss the true ones. In this paper, we develop a causal decision tree where nodes have causal interpretations. Our method follows a well established causal inference framework and makes use of a classic statistical test. The method is practical for finding causal signals in large data sets.
Survey of Widdringtonia Cederbergensis at Groot Koupoort, site 3219AC/11
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
Widdringtonia cedarbergensis
Widdringtonia wallichii
survey
map

description: This is a scanned copy of a survey, including a map, of Widdringtonia Cedarbergensis at Groot Koupoort, site 3219AC/11. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species.    Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape.   SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
On $p$-adic interpolation of motivic Eisenstein classes
Creators: name: Kings, Guido
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: In this paper we prove that the motivic Eisenstein classes associated to polylogarithms of commutative group schemes can be $p$-adically interpolated in étale cohomology. This generalizes results for elliptic curves obtained in our former work. Already for one dimensional commutative groups the results proved here are much more flexible as they allow to treat degeneration questions easily.
description: 24 pages, revised version
Supplementary documentation for SAEON's field instrument data collected at the Cape Peninsula Hospital Bend weather station
Creators: name: South African Environmental Observation Network (SAEON) Fynbos Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Cape Peninsula
Meteorological
Automatic Weather Station
Rainfall
air temperature
relative humidity
wind speed
wind direction
solar radiation
barometer

description: This package contains supporting information for the meteorological data collected at Cape Peninsula's Hospital Bend weather station, as part of the South African Environmental Observation Network's monitoring projects.
Coherent chemical kinetics as quantum walks I: Reaction operators for radical pairs
Creators: name: Chia, A.
name: Gorecka, A.
name: Tan, K. C.
name: Pawela, L.
name: Kurzynski, P.
name: Paterek, T.
name: Kaszlikowski, D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Classical chemical kinetics use rate-equation models to describe how a reaction proceeds in time. Such models are sufficient for describing state transitions in a reaction where coherences between different states do not arise, or in other words, a reaction which contain only incoherent transitions. A prominent example reaction containing coherent transitions is the radical-pair model. The kinetics of such reactions is defined by the so-called reaction operator which determines the radical-pair state as a function of intermediate transition rates. We argue that the well-known concept of quantum walks from quantum information theory is a natural and apt framework for describing multisite chemical reactions. By composing Kraus maps that act only on two sites at a time, we show how the quantum-walk formalism can be applied to derive a reaction operator for the standard avian radical-pair reaction. Our reaction operator predicts a recombination dephasing rate consistent with recent experiments [J. Chem. Phys. {\bf 139}, 234309 (2013)], in contrast to previous work by Jones and Hore [Chem. Phys. Lett. {\bf 488}, 90 (2010)]. The standard radical-pair reaction has conventionally been described by either a normalised density operator incorporating both the radical pair and reaction products, or by a trace-decreasing density operator that considers only the radical pair. We demonstrate a density operator that is both normalised and refers only to radical-pair states. Generalisations to include additional dephasing processes and an arbitrary number of sites are also discussed.
Leucadendron at site 3219AC/12
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
datasheet
density counts
Leucadendron pubescens
Leucadendron rubrum
Leucadendron salignum

description: This is a scanned copy of a datasheet on Leucadendron at site 3219AC/12, including density counts of Leucadendron pubescens, Leucadendron salignum and Leucadendron rubrum. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species.    Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape.   SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Feminist Approaches in Counselling Psychology: Empowering Women's Mental Health
Creators: name: Abidogun, Moruf Adebayo
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 440502
subject: Feminist methodologies
classificationCode: 520303
subject: Counselling psychology

description: This paper explores the application of feminist approaches in counselling psychology to empower women's mental health. It highlights the importance of considering gendered experiences, power dynamics, and societal influences on women's well-being. By examining the existing literature, this article identifies the key principles and interventions of feminist counselling psychology and their impact on women's empowerment. The paper concludes with recommendations for integrating feminist perspectives into counselling practices to promote positive mental health outcomes for women.
IRIS Observations of the Mg II h & k Lines During a Solar Flare
Creators: name: Kerr, Graham S.
name: Simões, Paulo J. A.
name: Qiu, Jiong
name: Fletcher, Lyndsay
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The bulk of the radiative output of a solar flare is emitted from the chromosphere, which produces enhancements in the optical and UV continuum, and in many lines, both optically thick and thin. We have, until very recently, lacked observations of two of the strongest of these lines: the Mg II h & k resonance lines. We present a detailed study of the response of these lines to a solar flare. The spatial and temporal behaviour of the integrated intensities, k/h line ratios, line of sight velocities, line widths and line asymmetries were investigated during an M class flare (SOL2014-02-13T01:40). Very intense, spatially localised energy input at the outer edge of the ribbon is observed, resulting in redshifts equivalent to velocities of ~15-26km/s, line broadenings, and a blue asymmetry in the most intense sources. The characteristic central reversal feature that is ubiquitous in quiet Sun observations is absent in flaring profiles, indicating that the source function increases with height during the flare. Despite the absence of the central reversal feature, the k/h line ratio indicates that the lines remain optically thick during the flare. Subordinate lines in the Mg II passband are observed to be in emission in flaring sources, brightening and cooling with similar timescales to the resonance lines. This work represents a first analysis of potential diagnostic information of the flaring atmosphere using these lines, and provides observations to which synthetic spectra from advanced radiative transfer codes can be compared.
description: 12 pages, 14 figures, Accepted for publication in Astronomy and Astrophysics
Population dynamics in Koue Bokkeveld, Paardekloof, site 3319AD/3
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
Koue Bokkeveld
Population dynamics

description: This is a scanned copy of a document noting the population dynamics in monitoring site 3319AD/3 in the Koue Bokkeveld. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species. Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).
Efficiency of Single Particle Engines
Creators: name: Proesmans, Karel
name: Driesen, Cedric
name: Cleuren, Bart
name: Broeck, Christian Van den
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the efficiency of a single particle Szilard and Carnot engine. Within a first order correction to the quasi-static limit, the work distribution is found to be Gaussian and the correction factor to average work and efficiency only depends on the piston speed. The stochastic efficiency is studied for both models and the recent findings on efficiency fluctuations are confirmed numerically. Special features are revealed in the zero temperature limit.
title: Regulation of kinesin KIFC1 and centrosome clustering by OTUD6B deubiquitylase
Creators: name: Sabat-Pospiech, Dorota Kaja
Publisher: name: University of Liverpool Repository
Year: 2023

description: Centrosome amplification is a hallmark of human cancers and is especially common in breast cancer, including triple-negative (TNBC) subtype. Centrosome amplification may lead to multipolar spindle formation and lethal multipolar mitosis. To avoid this, cancer cells often cluster their centrosomes to form a pseudo-bipolar spindle. This process relies on the kinesin KIFC1, which can be regulated by ubiquitin-mediated degradation. Deubiquitylases (DUBs) are a family of druggable enzymes, often dysregulated in cancer, which can remove ubiquitin from protein targets and rescue them from proteasomal degradation. Disruption of centrosome-clustering represents an attractive therapeutic approach for cancers with high centrosome amplification status, and one potential strategy may be targeting a KIFC1 regulatory DUB. 94 human DUBs were systematically tested for their effect on KIFC1 expression and centrosome clustering by two parallel siRNA screens. Co-analysis of two screens identified OTUD6B and JOSD2 as positive regulators of KIFC1 protein expression and centrosome clustering in the TNBC cell line BT549. Analysis of the TCGA breast cancer dataset demonstrates OTUD6B transcript is often overexpressed in breast cancer and correlates with worse survival which suggests a potential clinical relevance; thus, OTUD6B was selected for follow-up experiments. We show that OTUD6B depletion increases multipolar mitosis frequency in BT549, but its re-overexpression rescues bipolar spindle phenotype. OUTD6B localises to the centrosome and interacts with KIFC1 but is not affecting KIFC1 ubiquitylation in asynchronous cells. KIFC1 levels peaks at mitosis and is rapidly degraded during mitosis exit, OTUD6B follows a similar expression pattern. Preliminary data suggest that OTUD6B may stabilise KIFC1 specifically at mitosis. Furthermore, we establish KIF2A, a kinesin previously associated with the centrosome and bipolar spindle formation, as a common interactor of OTUD6B and KIFC1, potentially also regulated by OTUD6B. Finally, we show that BT549 cells with a high degree of centrosome amplification, but not healthy breast epithelial cells, are dependent on KIFC1 and OTUD6B for their survival. We also performed a pilot study to examine OTUD6B and KIFC1 expression, and centrosome amplification in uveal melanoma tissue samples. The research demonstrated that centrosome amplification is a frequent phenomenon in a subgroup of uveal melanomas and hence may be an attractive therapeutic target. In summary, our data suggest that, together with KIFC1, OTUD6B may be a promising novel target for anti-cancer specific therapies applicable for cancers with high centrosome amplification status such as TNCB and uveal melanoma.
title: A Clinical and Scientific Study to Investigate the Influence of Statins on Anastomotic Healing in Colorectal Surgery.
Creators: name: Battersby, Christopher
Publisher: name: University of Liverpool Repository
Year: 2021

description: Anastomotic leak remains one of the most devastating complications of colorectal surgery, as it is associated with increased morbidity and mortality, increased need for permanent stoma, increased risk of cancer recurrence, prolonged hospital admission and increased costs of healthcare. Anastomotic leak represents a failure of the complex process of tissue healing, therefore it must be regarded as a multifactorial complication, rather than as a single entity. Statins are amongst the most widely used drugs in the world, prescribed for the primary and secondary prevention of cardiovascular disease. Beyond lipid lowering, statins are known to have pleiotropic effects, which may exert a positive influence on processes fundamental to wound healing. Preliminary data from clinical studies suggests that statins may reduce the incidence of anastomotic leak. Hypothesis and Aims of this Study The hypothesis of this study is that statins promote processes fundamental to healthy tissue healing, and may therefore contribute to reducing the risk of anastomotic leak following colorectal surgery, and that the post-operative outcomes will be improved for patients taking statins. The aims of the study are to investigate whether statins exert an influence on colonic tissue healing. This thesis describes two studies run in parallel: a scientific study to investigate the effects of statins on primary cultured human colonic myofibroblasts, and a clinical study based on prospectively collected data from patients undergoing major colorectal surgery. Outcomes and Conclusions Atorvastatin, in concentrations equivalent to therapeutic doses, was shown to promote both the metabolic activity, and proliferation of primary cultured colonic myofibroblasts. Data was analysed from 113 patients in the clinical study, 38.9% of whom were taking statins at the time of the study. No difference was seen in the incidence of anastomotic leaks in patients taking statins, compared to those patients not taking statins, although the study population represented a relatively small cohort of patients with a low incidence of anastomotic leak (6 leaks out of 113 patients). The outcome from the clinical study raises the possibility that statins may represent a form of pharmacological prehabilitation, by normalising the risk of anastomotic leak in a population of patients with significant comorbidities, and a higher risk of anastomotic leak. The studies described in this thesis suggest that statins have an influence of processes fundamental to colonic tissue healing, and may contribute to reducing the risk of anastomotic leak. The potential direction for further studies to investigate this relationship is described.
Supplementary documentation for SAEON's field instrument data collected at the Cathedral Peak 2B station
Creators: name: South African Environmental Observation Network (SAEON) Grasslands-Forests-Wetlands Node
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: SAEON field instruments
Standard Operating Procedures
Calibration
Cathedral Peak
Meteorological
Tipping bucket
Precipitation

description: This package contains supporting information for the meteorological data collected at Cathedral Peak's 2B station, as part of the South African Environmental Observation Network's monitoring projects.
General survey of Widdringtonia Cederbergensis, site 3219AC
Creators: name: Jonkershoek Forestry Research Center
Publisher: name: South African Environmental Observation Network
Year: 2022
Subjects: Jonkershoek Forestry Research Centre
general survey
Widdringtonia cedarbergensis
Rainfall report
bird sightings
Widdringtonia wallichii

description: This is a scanned copy of a document of a general survey of Widdringtonia Cedarbergensis, site 3219AC, as well as a plant species list, bird sightings and rainfall reports. The Jonkershoek Forestry Research Center (part of the former South African Forestry Research Institute) was established in 1935 at Jonkershoek, near Stellenbosch, under the directorship of Dr C. L. Wicht. The initial aim was to determine how forestry activities in state plantations would affect climate, water conservation and erosion, and was later expanded to include studies of fynbos ecology, fire and alien species.    Studies from the 1930s to the early 1990s saw the accumulation of a large amount of data dealing with fire experiments, detailed vegetation plot surveys, rare plant surveys and ecological studies, hydrological studies and the development of management plans for catchments around the Western Cape. SAEON now houses the archive of data collected by the Jonkershoek Forestry Research Center, which was originally held by the Council for Scientific and Industrial Research (CSIR).