cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Imputation strategies for missing baseline neurological assessment covariates after traumatic brain injury: A CENTER-TBI study.
Creators: name: Ercole, Ari
name: Dixit, Abhishek
name: Nelson, David W
name: Bhattacharyay, Shubhayu
name: Zeiler, Frederick A
name: Nieboer, Daan
name: Bouamra, Omar
name: Menon, David K
name: Maas, Andrew I R
name: Dijkland, Simone A
name: Lingsma, Hester F
name: Wilson, Lindsay
name: Lecky, Fiona
name: Steyerberg, Ewout W
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021

description: Statistical models for outcome prediction are central to traumatic brain injury research and critical to baseline risk adjustment. Glasgow coma score (GCS) and pupil reactivity are crucial covariates in all such models but may be measured at multiple time points between the time of injury and hospital and are subject to a variable degree of unreliability and/or missingness. Imputation of missing data may be undertaken using full multiple imputation or by simple substitution of measurements from other time points. However, it is unknown which strategy is best or which time points are more predictive. We evaluated the pseudo-R2 of logistic regression models (dichotomous survival) and proportional odds models (Glasgow Outcome Score-extended) using different imputation strategies on the The Collaborative European NeuroTrauma Effectiveness Research in Traumatic Brain Injury (CENTER-TBI) study dataset. Substitution strategies were easy to implement, achieved low levels of missingness (<< 10%) and could outperform multiple imputation without the need for computationally costly calculations and pooling multiple final models. While model performance was sensitive to imputation strategy, this effect was small in absolute terms and clinical relevance. A strategy of using the emergency department discharge assessments and working back in time when these were missing generally performed well. Full multiple imputation had the advantage of preserving time-dependence in the models: the pre-hospital assessments were found to be relatively unreliable predictors of survival or outcome. The predictive performance of later assessments was model-dependent. In conclusion, simple substitution strategies for imputing baseline GCS and pupil response can perform well and may be a simple alternative to full multiple imputation in many cases.
Millihertz quasi-periodic oscillations and thermonuclear bursts from Terzan 5: A showcase of burning regimes
Creators: name: Linares, M.
name: Altamirano, D.
name: Chakrabarty, D.
name: Cumming, A.
name: Keek, L.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a comprehensive study of the thermonuclear bursts and millihertz quasi-periodic oscillations (mHz QPOs) from the neutron star (NS) transient and 11 Hz X-ray pulsar IGR J17480-2446, located in the globular cluster Terzan 5. The increase in burst rate that we found during its 2010 outburst, when persistent luminosity rose from 0.1 to 0.5 times the Eddington limit, is in qualitative agreement with thermonuclear burning theory yet opposite to all previous observations of thermonuclear bursts. Thermonuclear bursts gradually evolved into a mHz QPO when the accretion rate increased, and vice versa. The mHz QPOs from IGR J17480-2446 resemble those previously observed in other accreting NSs, yet they feature lower frequencies (by a factor ~3) and occur when the persistent luminosity is higher (by a factor 4-25). We find four distinct bursting regimes and a steep (close to inverse cubic) decrease of the burst recurrence time with increasing persistent luminosity. We compare these findings to nuclear burning models and find evidence for a transition between the pure helium and mixed hydrogen/helium ignition regimes when the persistent luminosity was about 0.3 times the Eddington limit. We also point out important discrepancies between the observed bursts and theory, which predicts brighter and less frequent bursts, and suggest that an additional source of heat in the NS envelope is required to reconcile the observed and expected burst properties. We discuss the impact of NS magnetic field and spin on the expected nuclear burning regimes, in the context of this particular pulsar.
description: Published in The Astrophysical Journal on 2012 March 9, Volume 748, Issue 2
title: Hematology-Oncology Transplant Nurses Experience Through the Moral Labyrinth of Integrating Palliative Care
Creators: name: Bennett, Taylor
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Hematology
subject: Oncology
subject: Nursing
subject: FOS: Health sciences
subject: Hematopoietic stem cell transplant
subject: Blood and marrow transplant
subject: Palliative care
subject: Early palliative care
subject: Moral distress
subject: Moral residue
subject: Moral injury
subject: Resilience
subject: Nursing
subject: Oncology

description: Early palliative care improves the quality of life for patients with hematological malignancies, yet the role of hematology-oncology transplant nurses in facilitating this care remains unclear. This study explored the experiences and understandings of 10 hematology-oncology transplant nurses from across Canada, working in both inpatient and ambulatory settings, regarding the early provision of palliative care for patients undergoing hematopoietic stem-cell transplantation. Findings revealed a complex understanding of palliative and end-of-life care, highlighting the emotional and moral challenges facing HOT nurses. The study provides new insights into how these nurses navigate the unique barriers to integrating palliative care into their specialized field, offering recommendations to improve interprofessional collaboration, education, and institutional support.
Watershed level baseline assessment in the Nariarlé watershed, Volta basin, Burkina Faso
Creators: name: K. Ouattara
name: S. Pare
name: S. Sawadogo-Kabore
name: S. Cinderby
name: A. De Bruin
Publisher: name: Gates Open Research
Year: 2019

description: Watershed level baseline assessment in the Nariarlé watershed, Volta basin, Burkina Faso
Coronal Magnetic Field Structure and Evolution for Flaring AR 11117 and its Surroundings
Creators: name: Tadesse, Tilaye
name: Wiegelmann, T.
name: Inhester, B.
name: Pevtsov, A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: In this study, photospheric vector magnetograms obtained with the Synoptic Optical Long-term Investigations of the Sun survey (SOLIS), are used as boundary conditions to model the three-dimensional nonlinear force-free (NLFF) coronal magnetic fields as a sequence of nonlinear force-free equilibria in spherical geometry. We study the coronal magnetic field structure inside active regions and its temporal evolution. We compare the magnetic field configuration obtained from NLFF extrapolation before and after flaring event in active region (AR) 11117 and its surroundings observed on 27 October 2010. We compare the magnetic field topologies and the magnetic energy densities and study the connectivities between AR 11117 and its surroundings. During the investigated time period, we estimate the change in free magnetic energy from before to after the flare to be 1.74x10^{32}erg which represents about 13.5% of nonlinear force-free magnetic energy before the flare. In this study, we find that electric currents from AR 11117 to its surroundings were disrupted after the flare.
description: 14 pages, 14 figures, Accepted by Solar Physics Journal
title: Mass- and Momentum-Conserved Secondary Injection Model (MMC-SIM) for Thrust Vector Control Analysis
Creators: name: Abdelwahab, Noreen
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Mass- and momentum-conserved secondary injection model (MMC-SIM)
subject: Thrust vector control (TVC)
subject: Computational fluid dynamics (CFD)
subject: rocket flight simulation
subject: Engineering--Aerospace

description: A mass- and momentum-conserved secondary injection model (MMC-SIM) is presented for thrust vector control (TVC) analysis in axisymmetric nozzles. TVC modelling provides fast thrust vector predictions for control and design applications. MMC-SIM addresses a key limitation in prior models - the lack of mass conservation, which often compromised accuracy through assumed jet exit conditions. Using a semi-empirical approach based on the blunt-body analogy, MMC-SIM uniquely incorporates both mass and momentum conservation for thrust vector predictions. Computational fluid dynamics (CFD) simulations were performed to verify that MMC-SIM captures the underlying physics of the flow, including boundary layer separation and the pressure distribution. MMC-SIM shows strong agreement with experimental results, yielding average and maximum lateral force prediction errors of 3.3% and 4.8%, respectively. Compared to current models, MMC-SIM halves the maximum error on the pressure-driven lateral force. MMC-SIM is highly suitable for integration into six degree-of-freedom rocket flight simulation programs.
AI-Assisted CT as a Clinical and Research Tool for COVID-19.
Creators: name: Tse, Zion Tsz Ho
name: Hovet, Sierra
name: Ren, Hongliang
name: Barrett, Tristan
name: Xu, Sheng
name: Turkbey, Baris
name: Wood, Bradford J
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Artificial intelligence
RT-PCR
Diagnosis
computed tomography
Covid-19

description: There is compelling support for widening the role of computed tomography (CT) for COVID-19 in clinical and research scenarios. Reverse transcription polymerase chain reaction (RT-PCR) testing, the gold standard for COVID-19 diagnosis, has two potential weaknesses: the delay in obtaining results and the possibility of RT-PCR test kits running out when demand spikes or being unavailable altogether. This perspective article discusses the potential use of CT in conjunction with RT-PCR in hospitals lacking sufficient access to RT-PCR test kits. The precedent for this approach is discussed based on the use of CT for COVID-19 diagnosis and screening in the United Kingdom and China. The hurdles and challenges are presented, which need addressing prior to realization of the potential roles for CT artificial intelligence (AI). The potential roles include a more accurate clinical classification, characterization for research roles and mechanisms, and informing clinical trial response criteria as a surrogate for clinical outcomes.
Modeling latent correlation structures with application to agricultural and environmental science
Creators: name: Bornn, Luke
Publisher: name: University of British Columbia
Year: 2012

description: In this thesis, we explore the issue of latent correlation structure in spatial and other correlated systems. Firstly, we propose a class of prior distributions on decomposable graphs, allowing for improved modeling flexibility. While existing methods solely penalize the number of edges, the proposed work empowers practitioners to control clustering, level of separation, and other features of the graph. Emphasis is placed on a particular prior distribution which derives its motivation from the class of product partition models; the properties of this prior relative to existing priors is examined through theory and simulation. We then demonstrate the use of graphical models in the field of agriculture, showing how the proposed prior distribution alleviates the inflexibility of previous approaches in properly modeling the interactions between the yield of different crop varieties. Secondly, we describe how spatial dependence can be incorporated into statistical models for crop yield along with the dangers of ignoring it. In particular, approaches that ignore this dependence suffer in their ability to capture (and predict) the underlying phenomena. Prior distributions are developed to accommodate the spatial non-stationarity arising from distinct between-region differences in agricultural policy and practice. As a result, the model developed has improved prediction performance relative to existing models, and allows for straightforward interpretation of climatic effects on the model's output. Lastly, we propose a novel approach to modeling nonstationary spatial fields. The proposed method works by expanding the geographic plane over which these processes evolve into higher dimensional spaces, transforming and clarifying complex patterns in the physical plane. By combining aspects of multi-dimensional scaling, group lasso, and latent variable models, a dimensionally sparse projection is found in which the originally nonstationary field exhibits stationarity. Following a comparison with existing methods in a simulated environment, dimension expansion is studied on a classic test-bed data set historically used to study nonstationary models. Following this, we explore the use of dimension expansion in modeling air pollution in the United Kingdom, a process known to be strongly influenced by rural/urban effects, amongst others, which gives rise to a nonstationary field.
Additional file 6 of Phylogenetic analysis and stress response of the plant U2 small nuclear ribonucleoprotein B″ gene family
Creators: name: Gao, Cong
name: Lu, Shuai
name: Zhou, Rong
name: Ding, Junjie
name: Fan, Jialiang
name: Han, Binying
name: Chen, Moxian
name: Wang, Baohua
name: Cao, Yunying
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 6: Table S5. Sequence summary of plant U2B″ protein-protein interaction network.
Virtual communities? the middle east revolutions at the Guardian forum: Comment Is Free
Creators: name: Kujawski, Bernard
name: Abell, Peter
Publisher: name: arXiv
Year: 2011
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: We investigate the possibility of virtual community formation in an online social network under a rapid increase of activity of members and newcomers. The evolution is studied of the activity of online users at the Guardian - Comment Is Free forum - covering topics related to the Middle East turmoil during the period of 1st of January 2010 to the 28th of March 2011. Despite a threefold upsurge of forum users and the formation of a giant component, the main network characteristics, i.e. degree and weight distribution and clustering coefficient, remained almost unchanged.
title: Pacts With Demons: Death, Conspiracy and the Internet
Creators: name: Chaudhry, Brennan
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Internet
subject: Conspiracy
subject: Labour
subject: Postmodernism
subject: Mass Communications
subject: Philosophy
subject: FOS: Philosophy, ethics and religion

description: As we have become more connected than ever, we find ourselves becoming less social than ever before. The internet has heralded the corrosion of working time and free time, self and other, and human versus machine. As users confront these different contradictions they are forced to reassess themselves, and try to generate an explanation with limited information and resources. If anything is clear, it seems that the internet is no longer the progressive, democratizing force that it was once promised as. The mutual co-creation of new social worlds has been replaced by duelling paranoia and narcissism, all while our data are bought, sold and analyzed behind our backs. Some users now claim that the internet is dead, populated only by bots, algorithmically generated content, and AI lurking behind a facade of endless feeds and targeted ads. This thesis seeks to understand this perspective, sympathetic to those who find themselves disenfranchised by the internet today, and critical of the infrastructure that enables it. In order to shed light on and describe this phenomenon, it investigates three case studies, each of which represents different instances that are cited as reasons for the supposed death of the internet, and involve artificial intelligence. These are, respectively, the presence of bots on social media platforms, the proliferation of AI generated media, and finally the ubiquity of AI powered algorithms and decision making systems in our lives. In his 1984 cyberpunk classic Neuromancer, William Gibson wrote “For thousands of years men dreamed of pacts with demons. Only now are such things possible” (p.165). This thesis seeks to understand the terms of that pact, what the demons are, and what we are giving up in exchange.
Weri Phonemes
Creators: name: Boxwell, Helen (Ed.)
name: Boxwell, Maurice (Ed.)
Publisher: name: Pacific Linguistics
Year: 1966

description: WERI PHONEMES. 77 0. Introduction 77 1. Inventory of Phonemes 77 1.1. Chart of Phonemic Norms 77 1.2. Description of Contrastive Features 78 2. Interpretation 78 2.1. Status of Items which may be either Consonant or Vowel 78 2.2. Status of Items which may be either Sequence or Unit 79 3. Description of Phonemes 81 3.1. Chart of Phoneme Sequences 81 3.2. Consonants 81 3.3. Vowels 85 3.4. Tone 87 3.5. Stress 88 4. Distribution of Phonemes 88 4.1. General 88 4.2. Specific 89 4.3. Frequency of Phonemes 90 5. Orthography 90 5.1. Proposed Orthography 90 5.2. List of Pidgin Words 91 5.3. Sample Text, in Phonetic and Orthographic Script 91Notes 93
Proof of Concept for the Autobiographical Memory Flexibility (MemFlex) Intervention for Posttraumatic Stress Disorder.
Creators: name: Moradi, Ali Reza
name: Piltan, Maryam
name: Choobin, Mohammad Hasan
name: Azadfallah, Parviz
name: Watson, Peter
name: Dalgleish, Tim
name: Hitchcock, Caitlin
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Randomized controlled trials
Cognitive Processes
Posttraumatic Stress Disorder
Autobiographical Memory
Open Data
Preregistered

description: Autobiographical memory distortions are a key feature of posttraumatic stress disorder (PTSD). In this proof-of-concept randomized controlled trial (N = 43), we evaluated an autobiographical memory flexibility intervention, MemFlex. We aimed to determine whether the mechanism-focused intervention, which aims to improve autobiographical memory processes, may also affect other cognitive predictors of PTSD and potentially reduce PTSD symptoms in Iranian trauma survivors diagnosed with PTSD. Results indicated significant, moderate to large between-groups effect sizes in favor of MemFlex, relative to wait-list control, for the targeted cognitive mechanism of autobiographical memory flexibility and PTSD symptoms. A large, significant effect was also observed on maladaptive posttraumatic cognitions-a strong predictor of PTSD prognosis, which is a key target of high-intensity cognitive therapies for PTSD. Findings support future completion of a scaled-up trial to evaluate treatment efficacy of MemFlex for PTSD to determine whether MemFlex may offer a culturally adaptive, low-cost, low-intensity intervention able to improve cognitive mechanisms of PTSD.
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19.
Creators: name: Bannerman, Bridget P
name: Júlvez, Jorge
name: Oarga, Alexandru
name: Blundell, Tom L
name: Moreno, Pablo
name: Floto, R Andres
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Humans
Drug Evaluation, Preclinical
Computational Biology
Models, Biological
Pandemics
Drug Development
COVID-19
SARS-CoV-2

description: Funder: Wellcome Trust
description: The coronavirus disease 2019 (COVID-19) pandemic caused by the new coronavirus (SARS-CoV-2) is currently responsible for more than 3 million deaths in 219 countries across the world and with more than 140 million cases. The absence of FDA-approved drugs against SARS-CoV-2 has highlighted an urgent need to design new drugs. We developed an integrated model of the human cell and SARS-CoV-2 to provide insight into the virus' pathogenic mechanism and support current therapeutic strategies. We show the biochemical reactions required for the growth and general maintenance of the human cell, first, in its healthy state. We then demonstrate how the entry of SARS-CoV-2 into the human cell causes biochemical and structural changes, leading to a change of cell functions or cell death. A new computational method that predicts 20 unique reactions as drug targets from our models and provides a platform for future studies on viral entry inhibition, immune regulation, and drug optimisation strategies. The model is available in BioModels (https://www.ebi.ac.uk/biomodels/MODEL2007210001) and the software tool, findCPcli, that implements the computational method is available at https://github.com/findCP/findCPcli.
Numerical methods for calculating poles of the scattering matrix with applications in grating theory
Creators: name: Bykov, Dmitry A.
name: Doskolovich, Leonid L.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Waveguide and resonant properties of diffractive structures are often explained through the complex poles of their scattering matrices. Numerical methods for calculating poles of the scattering matrix with applications in grating theory are discussed. A new iterative method for computing the matrix poles is proposed. The method takes account of the scattering matrix form in the pole vicinity and relies upon solving matrix equations with use of matrix decompositions. Using the same mathematical approach, we also describe a Cauchy-integral-based method that allows all the poles in a specified domain to be calculated. Calculation of the modes of a metal-dielectric diffraction grating shows that the iterative method proposed has the high rate of convergence and is numerically stable for large-dimension scattering matrices. An important advantage of the proposed method is that it usually converges to the nearest pole.
description: 9 pages, 2 figures, 4 tables
Ex vivo HIV entry into blood CD4+ T cells does not predict heterosexual HIV acquisition in women
Creators: name: Joag, Vineet
name: Sivro, Aida
name: Yende-Zuma, Nonhlanhla
name: Imam, Hajra
name: Samsunder, Natasha
name: Abdool Karim, Quarraisha
name: Abdool Karim, Salim
name: McKinnon, Lyle
name: Kaul, Rupert
Publisher: name: Columbia University
Year: 2018
Subjects: CD4 antigen
HIV infections—Prevention
HIV infections--Epidemiology
Epidemiology

description: Background
A blood-based assay that could quantify HIV susceptibility would be very valuable for HIV prevention research. Previously, we developed and validated an ex vivo, flow-based, HIV entry assay to assess genital HIV susceptibility in endocervical CD4+ T cells.

Methods
Here we assessed whether this tool could be used to predict HIV risk using blood-derived CD4+ T cells in a rigorously-blinded, nested case-control study using blood samples collected from high-risk, HIV-uninfected South African women enrolled in the CAPRISA 004 clinical trial. Cases, subsequently acquiring HIV were sampled prior to HIV infection and compared with controls, who remained HIV-uninfected. The primary endpoint was ex vivo entry of a CCR5-tropic HIV founder virus into blood CD4+ T cells. Secondary endpoints included HIV entry into CD4+ central (TCM) and effector (TEM) memory T cells, and into CD4+ T cell subsets expressing CCR5, CD69, CCR6, α4β1 or α4β7.

Results
Compared to bulk CD4+ T cells (4.9% virus entry), CD4+ T cells expressing CCR5, CCR6 or α4β1 and TEM were highly susceptible (15.5%, 8.8%, 8.2% and 10.8% entry, respectively, all p<0.0001), while TCM, CD69+ or α4β7+ CD4+ cells were moderately susceptible (6.4%, 6.0% and 5.8% respectively, p ≤ 0.003). While the proportion of the aforementioned highly susceptible cells correlated with overall virus entry into CD4+ T cells within an individual (r = 0.68, 0.47, 0.67, and 0.60 respectively, p<0.0001), blood virus entry did not predict subsequent mucosal HIV acquisition after controlling for sexual behaviour and condom use (OR 0.92, 95% CI 0.77–1.11, p = 0.40).

Conclusions
Although virus entry identified several previously known highly susceptible cellular HIV targets, blood HIV entry did not predict subsequent heterosexual HIV acquisition. Assessment of mucosal HIV susceptibility may require sampling at the site of HIV exposure.
Enumeration of nilpotent loops up to isotopy
Creators: name: Clavier, Lucien
Publisher: name: arXiv
Year: 2012
Subjects: subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 20N05

description: We modify tools introduced by Daniel Daly and Petr Vojtechovsky in order to count, for any odd prime q, the number of nilpotent loops of order 2q up to isotopy, instead of isomorphy.
description: 20 pages; important typos corrected (section 6)
Plagiomerus Crawford 1910
Creators: name: Noyes, John Stuart
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Encyrtidae
Plagiomerus

description: Key to Costa Rica species of Plagiomerus
 (Females)
1. Scutellum (Figs 47, 49, 50) medially with sculpture composed of uniform, punctate-reticulate cells and with 4 bristle-like or scale-like setae at apex (these conspicuously longer than other setae and suberect, normally slightly angled forwards).......... 2
- Scutellum (Figs 59, 65) medially with sculpture composed of non-uniform, longitudinally elongate, polygonal cells and with only one pair of bristle-like or scale-like subapical setae (these conspicuously longer than other setae and suberect, normally slightly angled forwards)...................................................................... 3
 2 (1) Antenna (Fig. 45) with F3 much smaller than F4 and without linear sensilla; two apical segments of clava paler than basal segment, generally yellowish, occasionally apical segment almost as dark as basal segment........................................................................................................ bangaloriensis Shafee, Alam & Agarwal (p. 43)
 - Antenna (Fig. 53) with F3 subequal to F4 and with linear sensilla; clava unicolorous brown........................................................................... hospes Timberlake (p. 45)
 3 (1) Funicle (Fig. 56) with F2 clearly larger than F1 and with linear sensilla..................................................................................................................... calabes sp.nov. (p. 49)
 - Funicle (Fig. 62, 63) with F2 slightly smaller than F1 and without linear sensilla.............................................................................................. peruviensis (Girault) (p. 51 )
description: Published as part of Noyes, John Stuart, 2023, ENCYRTIDAE OF COSTA RICA (HYMENOPTERA: CHALCIDOIDEA), 4 Subfamily Encyrtinae: tribes Arrhenophagini, Habrolepidini, Cerapterocerini, Cheiloneurini, Trechnitini, Cercobelini, Polaszekiini, Protyndarichoidini, Gahaniellini and Syrphophagini (part), mainly primary parasitoids and hyperparasitoids of Coccoidea and Psylloidea (Hemiptera), pp. 1-921 in Taxonomic Monographs on Neotropical Hymenoptera (Oxford, England) (Oxford, England) 2 (11) on pages 42-43, DOI: 10.5281/zenodo.8074943
title: Expanded Human Follicle Stem Cells For Use In Cartilage Repair
Creators: name: Sun, Haochen
Publisher: name: Schulich School of Engineering
Year: 2024
Subjects: subject: Stem cell
subject: Regenerative medicine
subject: Bioprocessing
subject: Osteoarthritis
subject: Cartilage repair
subject: Education--Sciences
subject: Biology
subject: Engineering--Biomedical

description: Osteoarthritis (OA) is a chronic joint disease characterized by the degeneration of articular cartilage and many groups are pursuing stem cells as a therapy for reversing this damage. Mesenchymal stem cells (MSCs) can be non-invasively derived from the base of hair follicles (hfMSCs), which have the potential to differentiate into chondrocytes in vitro, yet it remains unknown if these hfMSCs can affect cartilage repair in vivo. Another essential component in developing MSC-based therapies is obtaining a clinically relevant number of cells and this can be addressed with the utilization of stirred suspension bioreactors (SSBs), which facilitate higher fold expansion rates. Evaluating the behavior of hfMSCs in SSB culture is essential to validate their functional properties and therapeutic effects on cartilage repair in vivo compared to MSCs cultured in static 2D flasks. The first aim of this thesis was to compare trilineage differentiation potential, surface marker expressions, and proteomics analysis between static and SSB conditions to determine if these different culture conditions impacted MSCs phenotype/behaviour. Results suggested that hfMSCs from both conditions express similar surface markers and trilineage differentiation potential (adipocytes, osteoblasts, and chondrocytes), yet presented with distinct proteome profiles. The second aim focused on in vivo cartilage regeneration, wherein hfMSCs from both conditions (static vs. SSB culture) were injected into the knees of mice that received a full thickness cartilage injury. hfMSCs promoted a similar degree of cartilage regeneration regardless of culture condition and exhibited a beneficial therapeutic effect compared to the sham control group. This project underscores the importance of SSB expansion and its potential impact on hfMSCs functional properties, offering a scalable cell therapy option for patients suffering from OA.
Asymptotic expansion of beta matrix models in the one-cut regime
Creators: name: Borot, Gaëtan
name: Guionnet, Alice
Publisher: name: arXiv
Year: 2011
Subjects: subject: Probability (math.PR)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We prove the existence of a 1/N expansion to all orders in beta matrix models with a confining, off-critical potential corresponding to an equilibrium measure with a connected support. Thus, the coefficients of the expansion can be obtained recursively by the "topological recursion" of Chekhov and Eynard. Our method relies on the combination of a priori bounds on the correlators and the study of Schwinger-Dyson equations, thanks to the uses of classical complex analysis techniques. These a priori bounds can be derived following Boutet de Monvel, Pastur and Shcherbina, or for strictly convex potentials by using concentration of measure. Doing so, we extend the strategy of Guionnet and Maurel-Segala, from the hermitian models (beta = 2) and perturbative potentials, to general beta models. The existence of the first correction in 1/N has been considered previously by Johansson and more recently by Kriecherbauer and Shcherbina. Here, by taking similar hypotheses, we extend the result to all orders in 1/N.
description: 42 pages, 2 figures. v2: typos and a confusion of notation corrected. v3: version to appear in Commun. Math. Phys
Supplementary document for High-fidelity intensity diffraction tomography with a non-paraxial multiple-scattering model - 5994472.pdf
Creators: name: Zhu, Jiabei
name: Wang, Hao
name: Tian, Lei
Publisher: name: Optica Publishing Group
Year: 2022
Subjects: Uncategorized

description: Revised supplemental details of SSNP, BPM, bidirectional SSNP, memory-efficient auto-differentiation, and computational performance evaluation
Fast particle-mesh code for Milgromian dynamics
Creators: name: Visser, P. M.
name: Eijt, S. W. H.
name: de Nijs, J. V.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Modified Newtonian dynamics (MOND) is a promising alternative to dark matter. To further test the theory, there is a need for fluid- and particle-dynamics simulations. The force in MOND is not a direct particle-particle interaction, but derives from a potential for which a nonlinear partial differential equation (PDE) needs to be solved. Normally, this makes the problem of simulating dynamical evolution computationally expensive. We intend to develop a fast particle-mesh (PM) code for MOND (the AQUAL formalism). We transformed the nonlinear equation for MOND into a system of linear PDEs plus one algebraic equation. An iterative scheme with the fast Fourier transform (FFT) produces successively better numerical approximations. The algorithm was tested for dynamical systems in MOND where analytical solutions are known: the two-body problem, a body with a circular ring, and a spherical distribution of particles in thermal equilibrium in the self-consistent potential. The PM code can accurately calculate the forces at subpixel scale and reproduces the analytical solutions. Four iterations are required for the potential, but when the spatial steps are small compared to the kernel width, one iteration is suffices. The use of a smoothing kernel for the accelerations is inevitable in order to eliminate the self-gravity of the point particles. Our PDE solver is $15$ to $42$ times as slow as a standard Poisson solver. However, the smoothing and particle propagation takes up most of the time above one particle per $10^3$ pixels. The FFTs, the smoothing, and the propagation part in the code can all be parallelized.
description: 13 pages, 13 figures
Melting artificial spin ice
Creators: name: Kapaklis, Vassilios
name: Arnalds, Unnar B.
name: Harman-Clarke, Adam
name: Papaioannou, Evangelos Th.
name: Karimipour, Masoud
name: Korelis, Panagiotis
name: Taroni, Andrea
name: Holdsworth, Peter C. W.
name: Bramwell, Steven T.
name: Hjörvarsson, Björgvin
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Artificial spin ice arrays of micromagnetic islands are a means of engineering additional energy scales and frustration into magnetic materials. Despite much progress in elucidating the properties of such arrays, the `spins' in the systems studied so far have no thermal dynamics as the kinetic constraints are too high. Here we address this problem by using a material with an ordering temperature near room temperature. By measuring the temperature dependent magnetization in different principal directions, and comparing with simulations of idealized statistical mechanical models, we confirm a dynamical `pre-melting' of the artificial spin ice structure at a temperature well below the intrinsic ordering temperature of the island material. We thus create a spin ice array that has real thermal dynamics of the artificial spins over an extended temperature range.
Glucólisis y gluconeogénesis (Crucigrama)
Creators: name: Herráez, Angel
Publisher: name: Zenodo
Year: 2020
Subjects: metabolismo
glucólisis
gluconeogénesis
crucigrama
aprendizaje

description: Crucigrama para ayudar en el aprendizaje de las rutas metabólicas de síntesis y degradación de la glucosa.
Formulation of Metal-Organic Framework-Based Drug Carriers by Controlled Coordination of Methoxy PEG Phosphate: Boosting Colloidal Stability and Redispersibility.
Creators: name: Chen, Xu
name: Zhuang, Yunhui
name: Rampal, Nakul
name: Hewitt, Rachel
name: Divitini, Giorgio
name: O'Keefe, Christopher A
name: Liu, Xiewen
name: Whitaker, Daniel J
name: Wills, John W
name: Jugdaohsingh, Ravin
name: Powell, Jonathan J
name: Yu, Han
name: Grey, Clare P
name: Scherman, Oren A
name: Fairen-Jimenez, David
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021

description: Metal-organic framework nanoparticles (nanoMOFs) have been widely studied in biomedical applications. Although substantial efforts have been devoted to the development of biocompatible approaches, the requirement of tedious synthetic steps, toxic reagents, and limitations on the shelf life of nanoparticles in solution are still significant barriers to their translation to clinical use. In this work, we propose a new postsynthetic modification of nanoMOFs with phosphate-functionalized methoxy polyethylene glycol (mPEG-PO3) groups which, when combined with lyophilization, leads to the formation of redispersible solid materials. This approach can serve as a facile and general formulation method for the storage of bare or drug-loaded nanoMOFs. The obtained PEGylated nanoMOFs show stable hydrodynamic diameters, improved colloidal stability, and delayed drug-release kinetics compared to their parent nanoMOFs. Ex situ characterization and computational studies reveal that PEGylation of PCN-222 proceeds in a two-step fashion. Most importantly, the lyophilized, PEGylated nanoMOFs can be completely redispersed in water, avoiding common aggregation issues that have limited the use of MOFs in the biomedical field to the wet form-a critical limitation for their translation to clinical use as these materials can now be stored as dried samples. The in vitro performance of the addition of mPEG-PO3 was confirmed by the improved intracellular stability and delayed drug-release capability, including lower cytotoxicity compared with that of the bare nanoMOFs. Furthermore, z-stack confocal microscopy images reveal the colocalization of bare and PEGylated nanoMOFs. This research highlights a facile PEGylation method with mPEG-PO3, providing new insights into the design of promising nanocarriers for drug delivery.
Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex
Creators: name: Bove, Riley M.
name: Patrick, Ellis
name: Aubin, Cristin McCabe
name: Srivastava, Gyan
name: Schneider, Julie A.
name: Bennett, David A.
name: De Jager, Philip Lawrence
name: Chibnik, Lori B.
Publisher: name: Columbia University
Year: 2018
Subjects: Human reproduction--Endocrine aspects
Prefrontal cortex
Phosphorylation
Neurology
DNA--Methylation

description: Purpose
Human females have a unique duration of post-reproductive longevity, during which sex-specific mechanisms ma influence later-life mechanisms of neuronal resilience and vulnerability. The maintenance of energy metabolism, through the oxidative phosphorylation (OXPHOS) apparatus, is essential for brain health. Given the known association between reproductive period (years from menarche to menopause) and cognitive aging, we examined the hypothesis that cumulative estrogen exposure across the lifetime may be associated with differential methylation of genes in the OXPHOS pathway.

Methods
Using DNA methylation patterns in the post-mortem dorsolateral prefrontal cortex (DLPFC) of 426 women prospectively followed until death in the Religious Orders Study and Rush Memory and Aging Project, we examined the relationship between reproductive period (subtracting age at menarche from age at menopause) and DNA methylation of a published set of autosomal OXPHOS genes previously implicated in stroke susceptibility. We then performed an unsupervised analysis of methylation levels across the Hallmark pathways from the Molecular Signatures Database.

Results
We observed a strong association between reproductive period and DNA methylation status across OXPHOS CpGs. We replicated this association between reproductive period and DNA methylation in a much larger set of OXPHOS genes in our unsupervised analysis. Here, reproductive period also showed associations with methylation in genes related to E2F, MYC and MTORC1 signaling, fatty acid metabolism and DNA repair.

Conclusion
This study provides evidence from both a supervised and unsupervised analyses, that lifetime cumulative endogenous steroid exposures may play a role in maintenance of post-menopausal cellular balance, including in brain tissue.
Additional file 1 of Liquid biopsy at the frontier of detection, prognosis and progression monitoring in colorectal cancer
Creators: name: Zhou, Hui
name: Zhu, Liyong
name: Song, Jun
name: Wang, Guohui
name: Li, Pengzhou
name: Li, Weizheng
name: Luo, Ping
name: Sun, Xulong
name: Wu, Jin
name: Liu, Yunze
name: Zhu, Shaihong
name: Zhang, Yi
Publisher: name: figshare
Year: 2022
Subjects: Biophysics
Medicine
Molecular Biology
Biotechnology
Chemical Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer

description: Additional file 1.
The Phonemes of Iatmul
Creators: name: Staalsen, Philip (Ed.)
Publisher: name: Pacific Linguistics
Year: 1966

description: THE PHONEMES OF IATMUL. 69 0. Introduction 69 1. Chart of Phonemes 69 1.1. Vowels 69 1.2. Consonants 69 2. Vowel Phonemes 69 2.1. Allophones 70 2.2. Contrasts 70 3. Consonant Phonemes 70 3.1. Variants 71 3.2. Contrasts 72 4. Distribution of Phonemes Within the Syllable 72 5. Supra-segmental Features 74Notes 76Bibliography 76
title: Polygenic Risk Scores, Structural Brain Imaging and Quantitative Obsessive-Compulsive Symptom Scores in Clinically Diagnosed Samples of Children and Adolescents with Obsessive-Compulsive Disorder and other Neuropsychiatric Disorders
Creators: name: Antonyan, Lilit
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Pediatric
subject: mental health
subject: genetics
subject: neuroimaging
subject: Health Sciences

description: Obsessive-compulsive symptoms include intrusive thoughts and repetitive behaviors. They are common in youth and are reported to be moderately heritable and associated with structural brain changes implicated in their pathophysiology. This study explores the relationship between structural brain changes, genetic variation, and childhood obsessive-compulsive symptom scores in a sample comprising six different mental disorders. Genetic analysis showed potential correlations with large-scale summary statistics to identify relevant polygenic risk markers. We also observed a strong genetic association between obsessive-compulsive symptoms and polygenic risk for anxiety disorder. By analyzing brain imaging data including cortical thickness, surface area, and subcortical volume from clinically diagnosed cases and healthy controls, this research integrates polygenic risk score analysis to assess genetic susceptibility linked to OC traits. We delineate the surface area of the inferior parietal lobule as a promising neuroimaging endophenotype associated with obsessive-compulsive symptoms, revealing potential structural brain changes influenced by genetic markers. These findings contribute to understanding the biological pathophysiology of these traits in children and youth and sets the stage for further investigation in larger samples that may offer deeper insights into the etiology of obsessive-compulsive and other related neuropsychiatric disorders.
Glucólisis y gluconeogénesis (Crucigrama)
Creators: name: Herráez, Angel
Publisher: name: Zenodo
Year: 2019
Subjects: metabolismo
glucólisis
gluconeogénesis
crucigrama
aprendizaje

description: Crucigrama para ayudar en el aprendizaje de las rutas metabólicas de síntesis y degradación de la glucosa.
Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis
Creators: name: Hadjirin, Nazreen F.
name: Miller, Eric L.
name: Murray, Gemma G. R.
name: Yen, Phung L. K.
name: Phuc, Ho D.
name: Wileman, Thomas M.
name: Hernandez-Garcia, Juan
name: Williamson, Susanna M.
name: Parkhill, Julian
name: Maskell, Duncan J.
name: Zhou, Rui
name: Fittipaldi, Nahuel
name: Gottschalk, Marcelo
name: Tucker, A. W. ( Dan)
name: Hoa, Ngo Thi
name: Welch, John J.
name: Weinert, Lucy A.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: subject: Research Article
subject: Genotype to phenotype
subject: Prediction model
subject: Ecology
subject: FOS: Biological sciences
subject: Beta-lactam resistance
subject: Tiamulin
subject: Trimethoprim
subject: Pig

description: Abstract: Background: Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. Results: We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into ‘resistant’ and ‘susceptible’, highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. Conclusions: We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
Stable Lorentzian Wormholes in Dilatonic Einstein-Gauss-Bonnet Theory
Creators: name: Kanti, Panagiota
name: Kleihaus, Burkhard
name: Kunz, Jutta
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss the properties of Lorentzian wormholes in dilatonic Einstein-Gauss-Bonnet theory in four spacetime dimensions. These wormholes do not need any form of exotic matter for their existence. A subset of these wormholes is shown to be linearly stable with respect to radial perturbations. We perform a comprehensive study of their domain of existence, and derive a generalised Smarr relation for these wormholes. We also investigate their geodesics determining all possible particle trajectories, and perform a study of the acceleration and tidal forces that a traveler crossing the wormhole would feel.
description: 29 pages, 18 figures, typos corrected, version published in Physical Review D
An improvement on the base-change theorem and the functor $f^!$
Creators: name: Neeman, Amnon
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14F05 (Primary), 13D09, 18G10 (Secondary)

description: The major improvement in this paper is that we can extend the functor $(-)^!$ of Grothendieck duality to the unbounded derived category of sufficiently nice algebraic stacks. The original motivation came from formulas discovered by Avramov and Iyengar, linking Grothendieck duality with Hochscild homology and cohomology.
description: 159 pages. This is the final, published version