cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comments on the d-wave pairing mechanism for cuprate high $T_c$ superconductors: Higher is different?
Creators: name: Choi, Han-Yong
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: The question of pairing glue for the cuprate superconductors (SC)is revisited and its determination through the angle resolved photo-emission spectroscopy (ARPES) is discussed in detail. There are two schools of thoughts about the pairing glue question: One argues that superconductivity in the cuprates emerges out of doping the spin singlet resonating valence bond (RVB) state. Since singlet pairs are already formed in the RVB state there is no need for additional boson glue to pair the electrons. The other instead suggests that the d-wave pairs are mediated by the collective bosons like the conventional low $T_c$ SC with the alteration that the phonons are replaced by another kind of bosons ranging from the antiferromagnetic (AF) to loop current fluctuations. An approach to resolve this dispute is to determine the frequency and momentum dependences of the diagonal and off-diagonal self-energies directly from experiments like the McMillan-Rowell procedure for the conventional SC. In that a simple d-wave BCS theory describes superconducting properties of the cuprates well, the Eliashberg analysis of well designed high resolution experimental data will yield the crucial frequency and momentum dependences of the self-energies. This line of approach using ARPES are discussed in more detail in this review, and some remaining problems are commented.
description: Invited review article published in the Journal of Korean Physical Society; several typos corrected and a few comments and references added
title: Constraining the Magneto-Ionic Environment of Galactic Supernova Remnants
Creators: name: Scullion, Larson
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Astronomy and Astrophysics

description: The Galactic Magnetic Field (GMF) plays a crucial role in the evolution of the Milky Way, influencing where stars can be born and supporting large-scale structures. Despite this, relatively little is known about the GMF, prompting many efforts to map and constrain the magnetic field strength and direction in as much of the sky as possible. One of the most useful analysis tools for doing so is the observation of rotation measures (RMs), a quantity describing the effects of Faraday rotation on polarised radiation that depends on the magnetic field threading the volume of electron gas the radiation travels through. By calculating RMs from polarised sources at known distances, we are able to deduce properties of the GMF, provided that we know the distribution of electrons along the light propagation path. Historically, this technique is most often applied to unresolved compact sources, but analysis of these sources only provide us information about the line-of-sight magnetic field. My research focuses on applying a similar technique to supernova remnants (SNRs), extended sources of polarised emission in our Galaxy, in order to determine `anchor points' of the GMF where the 3-dimensional magnetic field can be found. I refined existing work using SNRs to develop techniques of depolarisation analysis and RM gradient analysis that constrain the GMF and provide necessary context for the magneto-ionic environment around these objects.
Waiting for the better reward: Comparison of delay of gratification in young children across two cultures
Creators: name: Ding, Ning
name: Frohnwieser, Anna
name: Miller, Rachael
name: Clayton, Nicola S.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: subject: Research Article
subject: Biology and life sciences
subject: Social sciences
subject: FOS: Social sciences
subject: People and places
subject: Medicine and health sciences

description: Funder: FP7 Ideas: European Research Council; funder-id: http://dx.doi.org/10.13039/100011199; Grant(s): 3399933
description: Funder: China Scholarship Council, China
description: Delay of gratification–a form of self-control–is the ability to forsake immediately available rewards in order to obtain larger-valued outcomes in future, which develops throughout the pre-school years. The majority of previous research in this area has been conducted with Western populations, therefore knowledge of Eastern children’s performance is scarcer. Here, utilising on a recently published dataset of British children (n = 61), we further tested delay of gratification in 3 to 5-year-old Chinese children (n = 75) using Bramlett et al.’s (2012) delay choice paradigm. The paradigm was previously used in non-human primates and it featured a mechanized rotating tray that sequentially moves rewards within reach. Additionally, we administered 3 inhibitory control tasks and 1 standardised delay choice task to Chinese pre-schoolers (British children were not tested). We aimed to investigate the influence of culture, reward type and reward visibility on pre-schoolers’ ability to delay gratification. We found significant age-related improvements in delay of gratification ability in both countries and children performed better when presented with rewards varying in quality than quantity. Consistent with previous cross-cultural literature, Chinese children showed better overall performance than their British peers when reward visibility was manipulated (though reward visibility itself had no significant effect on performance). There were significant correlations in Chinese children’s performance in Bramlett et al.’s (2012) delay choice paradigm and performance in some (though not all tested) inhibitory control tasks. We discuss these results in relation to task demands and the broader social orientation of self-control. We concluded that the intuitive comparative assessment of self-control task taps into children’s delay of gratification ability. Our results emphasize the importance of testing for socio-cultural influences on children’s cognitive development.
The surface chemistry of chalcopyrite during electrochemical dissolution
Creators: name: Ghahremaninezhad Gharelar, Ahmad
Publisher: name: University of British Columbia
Year: 2012

description: Hydrometallurgy may be an alternative to the currently practiced smelting process for copper extraction from chalcopyrite (CuFeS₂). However, the low temperature hydrometallurgical processes for chalcopyrite continue to face challenges, mostly relating to their slow dissolution rates or high sulfuric acid production. The slow dissolution rate of the mineral is strongly linked to the formation of the passive film on its surface. However, despite 40 years of research on this topic, there is still not a complete agreement between researchers about the composition and stability of chalcopyrite’s passive film in sulfuric acid solutions. In this work, the nature of chalcopyrite’s passive film and its stability were studied by application of a variety of electrochemical techniques. Additionally, the electrochemical results of the chalcopyrite study were compared to those obtained for a pyrrhotite electrode (Fe₁₋xS), as pyrrhotite electrochemistry represents a simplified case of the chalcopyrite system. X-ray photoelectron spectroscopy (XPS) was used to analyze the composition of the product layers formed on the surface. It is shown that the chalcopyrite electrode is passive for potentials up to 0.90 VSHE. Above this potential, transpassive dissolution occurs. Results of XPS studies have suggested that a metal-deficient sulfide film (Cu₁₋xFe₁₋yS₂₋z) is the most plausible copper and iron containing sulfide phase which passivates the surface of chalcopyrite. In addition, an outer layer of iron oxyhydroxide (FeOOH) forms on the passive film. FeOOH forms via oxidation of the passive film’s ferrous sulfide phases. The thickness of the sulfide passive film was calculated to be approximately 6.7 nm. It is demonstrated that the transpassive dissolution of chalcopyrite is significantly linked to oxidation of sulfur (from sulfide in the passive film to elemental sulfur and maybe sulfur species with higher oxidation states, e.g. thiosulfate). No elemental sulfur or polysulfide species were detected on the surface for potentials below 0.90 VSHE.
The project to understand and research preterm pregnancy outcomes and stillbirths in South Asia (PURPOSe): a protocol of a prospective, cohort study of causes of mortality among preterm births and stillbirths
Creators: name: McClure, Elizabeth M.
name: Saleem, Sarah
name: Goudar, Shivaprasad S.
name: Dhaded, Sangappa
name: Guruprasad, G.
name: Kumar, Yogesh
name: Tikmani, Shiyam S.
name: Kadir, Masood
name: Raza, Jamal
name: Yasmin, Haleema
name: Moore, Janet L.
name: Kim, Jean
name: Bann, Carla
name: Parlberg, Lindsay
name: Aceituno, Anna
name: Carlo, Waldemar A.
name: Silver, Robert M.
name: Lamberti, Laura
name: Patterson, Janna
name: Goldenberg, Robert L.
Publisher: name: Columbia University
Year: 2018
Subjects: Reproductive health
Newborn infants--Mortality
Stillbirth
Premature infants
Epidemiology

description: Background
                In South Asia, where most stillbirths and neonatal deaths occur, much remains unknown about the causes of these deaths. About one-third of neonatal deaths are attributed to prematurity, yet the specific conditions which cause these deaths are often unclear as is the etiology of stillbirths. In low-resource settings, most women are not routinely tested for infections and autopsy is rare.

                Methods
                This prospective, cohort study will be conducted in hospitals in Davengere, India and Karachi, Pakistan. All women who deliver either a stillbirth or a preterm birth at one of the hospitals will be eligible for enrollment. With consent, the participant and, when applicable, her offspring, will be followed to 28-days post-delivery. A series of research tests will be conducted to determine infection and presence of other conditions which may contribute to the death. In addition, all routine clinical investigations will be documented. For both stillbirths and preterm neonates who die ≤ 28 days, with consent, a standard autopsy as well as minimally invasive tissue sampling will be conducted. Finally, an expert panel will review all available data for stillbirths and neonatal deaths to determine the primary and contributing causes of death using pre-specified guidance.

                Conclusion
                This will be among the first studies to prospectively obtain detailed information on causes of stillbirth and preterm neonatal death in low-resource settings in Asia. Determining the primary causes of death will be important to inform strategies most likely to reduce the high mortality rates in South Asia.

Trial registration
Clinicaltrials.gov (NCT03438110) Clinical Trial Registry of India (CTRI/2018/03/012281).
title: Mass Transfer Fundamentals in Complex Systems
Creators: name: Mayorga Ariza, Maria Daniela
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Mass Transfer
subject: Diffusion Coefficient
subject: Solvents
subject: Solvent-Assisted Recovery Methods
subject: Bitumen
subject: CT Scanner
subject: Engineering--Petroleum
subject: Engineering--Chemical
subject: Engineering

description: Mass transfer plays a critical role in most engineering processes, significantly affecting production, processing efficiency, and overall economic outcomes. In the context of thermal recovery of heavy oil using solvents, accurately estimating diffusion coefficients is vital for effective project design. Calculating diffusion coefficients is a meticulous process that requires precise experimental work and data acquisition to ensure reliability. These coefficients are essential for designing and analyzing thermal recovery techniques, such as solvent-assisted steam approaches, where decisions regarding rates, solvent proportions, and types depend heavily on accurate diffusion data. It is crucial to consider the influential role of water, which is present in most reservoirs and significantly impacts mass transfer, often without being fully acknowledged. Previous research on multiphase mass transfer has primarily focused on atmospheric conditions and liquid solvents. However, this study examines mass transfer from gaseous solvents to heavy oil in the presence of a water layer at elevated pressures. Specifically, the behaviors of solvents such as dimethyl ether (DME), propane, and CO₂ are compared, investigating the effects of increased pressures and varying solvent-to-oil ratios. Computed Tomography (CT) imaging is employed to monitor the initial stages of the diffusion process, providing a detailed understanding of these complex interactions. The results obtained are then compared with the behavior of these solvents in a biphasic system with heavy oil but without a water layer. This comparative analysis highlights the role of the water layer, contributing to the optimization of thermal recovery processes. This study represents an advancement in understanding diffusion processes and their influence on thermal recovery methods. The findings provide a foundation for developing more efficient and sustainable methods of heavy oil extraction, highlighting the crucial role of water in the mass transfer process.
Improving pregnancy outcomes in low- and middle-income countries
Creators: name: Goldenberg, Robert L.
name: McClure, Elizabeth M.
name: Saleem, Sarah
Publisher: name: Columbia University
Year: 2018
Subjects: Mothers--Mortality
Newborn infants--Mortality
Pregnancy
Reproductive health
Obstetrics
Poor--Health and hygiene
Stillbirth

description: This paper reviews the very large discrepancies in pregnancy outcomes between high, low and middle-income countries and then presents the medical causes of maternal mortality, stillbirth and neonatal mortality in low-and middle-income countries. Next, we explore the medical interventions that were associated with the very rapid and very large declines in maternal, fetal and neonatal mortality rates in the last eight decades in high-income countries. The medical interventions likely to achieve similar declines in pregnancy-related mortality in low-income countries are considered. Finally, the quality of providers and the data to be collected necessary to achieve these reductions are discussed. It is emphasized that single interventions are unlikely to achieve important reductions in pregnancy-related mortality. Instead, improving the overall quality of pregnancy-related care across the health-care system will be necessary. The conditions that cause maternal mortality also cause stillbirths and neonatal deaths. Focusing on all three mortalities together is likely to have a larger impact than focusing on one of the mortalities alone.
Emergent Critical Phase and Ricci Flow in a 2D Frustrated Heisenberg Model
Creators: name: Orth, Peter P.
name: Chandra, Premala
name: Coleman, Piers
name: Schmalian, Jörg
Publisher: name: arXiv
Year: 2012
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We introduce a two-dimensional frustrated Heisenberg antiferromagnet on interpenetrating honeycomb and triangular lattices. Classically the two sublattices decouple, and "order from disorder" drives them into a coplanar state. Applying Friedan's geometric approach to nonlinear sigma models, we show that the scaling of the spin-stiffnesses corresponds to the Ricci flow of a 4D metric tensor. At low temperatures, the relative phase between the spins on the two sublattices is described by a six-state clock model with an emergent critical phase.
description: 4+ pages, 2 figures
title: Multi-fidelity Aerodynamic Analysis of Outboard Horizontal Stabilizers for Small-scale Aircraft
Creators: name: De Alwis, Arjuna
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Outboard Horizontal Stabilizer
subject: CFD
subject: LLT
subject: Induced drag
subject: Engineering--Aerospace
subject: Engineering--Mechanical

description: The Outboard Horizontal Stabilizer (OHS) configuration is a unique fixed-wing design often used when a traditional tail is impractical and has been proposed as a means to achieve enhanced range and endurance. This study utilized a mixture of numerical approaches to quantify and critically examine the potential performance gains of the OHS concept. A modified non-linear lifting-line approach incorporating wing interactions was used for a fast low-fidelity model, and Reynolds Averaged Navier Stokes simulations were completed using OpenFOAM. A representative small-scale wing-tail combination was arranged into traditional, outboard, split, and extended span configurations and was used as a case study. The results obtained in this work demonstrate a substantial increase in Cl/Cd and Cl^{3/2}/Cd ratios for the OHS when compared to configurations with a similar main wing span, correlating to increased range and endurance, respectively. However, it was observed that simply extending the main wing to the overall span of the OHS configuration yielded higher performance. The importance of performing an aerodynamic analysis while considering static stability and trim is also discussed in detail. Furthermore, the specific conditions that can lead to increased overall lift and reduced induced drag on the stabilizers are highlighted and discussed using different approaches, and a qualitative analysis of the wake flow field was used to explain and confirm conclusions. Finally, a focused parametric study was performed to analyze how stabilizer position and deflection impact aerodynamic performance. It was found that for a fixed tail arm, having the tail just outboard of the main wing would maximize the performance of an OHS configuration. It was further found that the lift-to-drag ratio of an OHS configuration may surpass that of a conventional configuration with the same overall span if the fraction of tail span is reduced while increasing the tail arm, in order to maintain stability. Future studies will focus on a comprehensive optimization analysis to examine when and how OHS configurations may outperform optimal conventional configurations.
title: Exploring the Impact of a Virtual Simulation on Nursing Students’ Clinical Judgment During Patient Deterioration in Oncology
Creators: name: Fox, Catherine Elizabeth
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Virtual simulation
subject: Education--Curriculum and Instruction
subject: Nursing
subject: FOS: Health sciences
subject: Oncology

description: To improve patient outcomes during emergent situations, nurses require strong clinical judgment to recognize, assess, and intervene to make appropriate decisions. Unfortunately, it can be challenging to provide nursing students with the necessary knowledge to utilize skills such as clinical judgment in complex emergency situations. Limited access to clinical experiences, particularly in oncology, leaves many students unprepared to manage deteriorating patients after graduation. Virtual simulation has emerged as a promising educational strategy, enabling students to apply knowledge, develop critical thinking skills, and gain competence in a safe environment. This mixed-methods study evaluated the impact of a virtual simulation on nursing students’ clinical judgment during patient deterioration in oncology. Quantitative assessments measured changes in clinical judgment before, during, and after the simulation, while a qualitative reflective questionnaire captured students' insights into their decision-making processes. Quantitative data demonstrated improvements in students' decision-making abilities, particularly in recognizing and addressing early signs of patient deterioration in oncology. Qualitative responses indicated that students felt more confident and better able to bridge theoretical knowledge with clinical practice, an essential outcome for building clinical decision making. Findings from this study suggest that virtual simulation may enhance nursing students' clinical judgment by providing a structured and safe environment for skill development. The results support virtual simulation as a practical approach for strengthening the development of clinical judgment in nursing education, advancing patient safety, and improving quality of care in oncology nursing.
Long-term magnetic field monitoring of the Sun-like star ξBootis A
Creators: name: Morgenthaler, A.
name: Petit, P.
name: Saar, S.
name: Solanki, S. K.
name: Morin, J.
name: Marsden, S. C.
name: Auriere, M.
name: Dintrans, B.
name: Fares, R.
name: Gastine, T.
name: Lanoux, J.
name: Lignieres, F.
name: Paletou, F.
name: Velez, J. C. Ramirez
name: Theado, S.
name: Van Grootel, V.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Aims. We aim to investigate the long-term temporal evolution of the magnetic field of the solar-type star ξBootis A, both from direct magnetic field measurements and from the simultaneous estimate of indirect activity indicators. Methods. We obtained seven epochs of high-resolution, circularly-polarized spectra from the NARVAL spectropolarimeter between 2007 and 2011, for a total of 76 spectra. Using approximately 6,100 photospheric spectral lines covering the visible domain, we employed a cross-correlation procedure to compute a mean polarized line profile from each spectrum. The large-scale photospheric magnetic field of the star was then modelled by means of Zeeman-Doppler Imaging, allowing us to follow the year-to-year evolution of the reconstructed magnetic topology. Simultaneously, we monitored the width of several magnetically sensitive spectral lines, the radial velocity, the line asymmetry of intensity line profiles, and the chromospheric emission in the cores of the Ca II H and Halpha lines. Results. During the highest observed activity states, in 2007 and 2011, the large-scale field of ξBoo A is almost completely axisymmetric and is dominated by its toroidal component. The magnetic topologies reconstructed for these activity maxima are very similar, suggesting a form of short cyclicity in the large-scale field distribution. Correlated temporal evolution, due to both rotational modulation and seasonal variability, is observed between the Ca II emission, the Halpha emission and the width of magnetically sensitive lines. When measurable, the differential rotation reveals a strong latitudinal shear in excess of 0.2 rad/d.
description: 16 pages, 8 figures, accepted for publication in A&A, abstract shortened to respect the 1920 characters required
title: Insights on Methane and Carbon Dioxide Concentrations in Glacial Meltwater from Athabasca, Dome and Robertson Glaciers: Canadian Rockies
Creators: name: Kersey, Crystal
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: glaciers
subject: Canadian Rockies
subject: greenhouse gas
subject: subglacial processes
subject: carbon cycling
subject: Physical Geography
subject: Geochemistry
subject: FOS: Earth and related environmental sciences

description: This study addresses the research gap in the understanding of CO2 and CH4 dynamics in alpine glaciers, where limited studies have been conducted, particularly in terms of spatial and temporal coverage. Previous research often focused on single-point sampling in the glacial forefield over a few consecutive days during the melt season, leaving significant uncertainty about the broader patterns and controls on dissolved gasses in glacial environments. To overcome these limitations, this study conducted extensive sampling during the 2023 melt season at Athabasca, Dome, and Robertson Glaciers in the Canadian Rockies. Four locations at each glacier were sampled during three different visits spread throughout the melt season, allowing for a comprehensive analysis of the temporal and spatial variability in dissolved gas concentrations. The study analyzed a range of parameters, including: dissolved CO2 and CH4 concentrations through headspace equilibration, dissolved inorganic carbon (DIC), dissolved organic carbon (DOC), major ions, pH, electrical conduc-tivity, dissolved oxygen, oxidation-reduction potential (ORP), and suspended sediment concentration. A spearman r correlation matrix was used to further investigate geochemical relationships to greenhouse gas concentrations. The re-sults revealed that CO2 was consistently undersaturated across all sites, suggesting a net uptake of atmospheric CO2 by the meltwaters. Low CO2 likely relates to mineral weathering reactions with the carbonate-based bedrock. In contrast, CH4 was found to be supersaturated at 41 of the 49 sites, with the remaining eight sites having CH4 concentrations below the detection limit. CO2 concentrations were lowest at Athabasca Glacier and varied across the melt season, with increases correlated to parameters that suggest longer meltwater residence times. Methane concentrations were inversely correlated with ORP, indicating that more reductive conditions in subglacial environments may enhance CH4 production or limit its oxidation. This study provides new insights into the biogeochemical processes governing CO2 and CH4 dynamics in glacial meltwaters and underscores the significance of extensive spatial and temporal sampling in understanding these dy-namics. The findings contribute to the understanding of the role of alpine glaciers in carbon cycling and the potential release of greenhouse gasses.
Comparing COVID-19 risk factors in Brazil using machine learning: the importance of socioeconomic, demographic and structural factors.
Creators: name: Baqui, Pedro
name: Marra, Valerio
name: Alaa, Ahmed M
name: Bica, Ioana
name: Ercole, Ari
name: Van Der Schaar, Mihaela
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Humans
Hospitalization
Hospital Mortality
Models, Biological
Socioeconomic Factors
Brazil
Female
Male
Pandemics
Machine Learning
COVID-19
SARS-CoV-2

description: The COVID-19 pandemic continues to have a devastating impact on Brazil. Brazil's social, health and economic crises are aggravated by strong societal inequities and persisting political disarray. This complex scenario motivates careful study of the clinical, socioeconomic, demographic and structural factors contributing to increased risk of mortality from SARS-CoV-2 in Brazil specifically. We consider the Brazilian SIVEP-Gripe catalog, a very rich respiratory infection dataset which allows us to estimate the importance of several non-laboratorial and socio-geographic factors on COVID-19 mortality. We analyze the catalog using machine learning algorithms to account for likely complex interdependence between metrics. The XGBoost algorithm achieved excellent performance, producing an AUC-ROC of 0.813 (95% CI 0.810-0.817), and outperforming logistic regression. Using our model we found that, in Brazil, socioeconomic, geographical and structural factors are more important than individual comorbidities. Particularly important factors were: The state of residence and its development index; the distance to the hospital (especially for rural and less developed areas); the level of education; hospital funding model and strain. Ethnicity is also confirmed to be more important than comorbidities but less than the aforementioned factors. In conclusion, socioeconomic and structural factors are as important as biological factors in determining the outcome of COVID-19. This has important consequences for policy making, especially on vaccination/non-pharmacological preventative measures, hospital management and healthcare network organization.
Additional file 3 of The MLR, NLR, PLR and D-dimer are associated with clinical outcome in lung cancer patients treated with surgery
Creators: name: Wang, Jun
name: li, Huawei
name: Xu, Ran
name: Lu, Tong
name: Zhao, Jiaying
name: Zhang, Pengfei
name: Qu, Lidong
name: Zhang, Shengqiang
name: Guo, Jida
name: Zhang, Linyou
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: Science Policy
subject: Hematology

description: Additional file 3. After postoperative adjuvant medication,relationship between high and low groups of MLR, NLR, PLR and D-Dimer and survival time of patients.
title: Characterizing Determinants of Species Barrier in Prion Infection Using Gene-edited Cell Culture Models
Creators: name: Rahimi Aqdam, ShabBoo
Publisher: name: Cumming School of Medicine
Year: 2024
Subjects: subject: CAD5 cells
subject: prion protein (PrP)
subject: species barrier
subject: lentviral transducton
subject: Chronic Wastng Disease (CWD)
subject: camel prion disease
subject: gene-edited cell models
subject: Biology--Cell
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biology--Molecular

description: Prion diseases, fatal neurodegeneraƟve disorders, are caused by the misfolded isoform of the prion protein (PrPSc), which can propagate and induce prion disease across different species. The primary aim of this study was to establish a cell model for invesƟgaƟng the prion propagaƟon in various species, including camel and cervids. A major obstacle in studying prion diseases is the "species barrier," where prion transmission between species is inhibited due to structural mismatches between the normal host prion protein (PrPC) and the infecƟous isoform, PrPSc. Overcoming this barrier is crucial for studying emerging prion diseases, such as Chronic WasƟng Disease (CWD) and Camel prion disease. Another key obstacle is “dominant-negaƟve inhibiƟon of prion replicaƟon”, where endogenous PrP, such as mouse PrP, can negaƟvely interfere with exogenous prion infecƟon. Therefore, it is essenƟal to first confirm the complete knockout (KO) of endogenous PrP in our cell culture system, then transduce species-specific PrP into the KO cells. To achieve this, we first confirmed the complete knockout of endogenous mouse PrP in a CAD5 subclone by performing bacterial gene cloning, sequencing, and INDEL idenƟficaƟon. Then, we used lenƟviral transducƟon to introduce PrP genes from mouse, bank vole, cervid, and camel into the neuronal CAD5-KO cells. Immunoblot analysis confirmed successful PrP expression in these gene-edited cells, thereby overcoming the species barrier. Fluorescent imaging and Fluorescence- AcƟvated Cell SorƟng (FACS) were used to further characterize and enrich the cells for high PrP expression. Subsequently, we challenged these engineered cell models with brain homogenates from prion-infected animals to study prion infecƟon. Notably, for the first Ɵme, we report the detecƟon of PrPSc in camel-PrP-expressing cells infected with camel prions. AddiƟonally, cervid-PrP-expressing cells infected with CWD prions showed the presence of PrPSc bands in immunoblot analysis, validaƟng prion propagaƟon in our cervid model. This is the first evidence of successful camel prion propagaƟon in a cell model, demonstraƟng the ability of these engineered cells to overcome the species barrier. Overall, this model provides a novel plaƞorm for studying prion biology and cross-species transmission.
Quantum current noise from a Born-Markov master equation
Creators: name: Kirton, P. G.
name: Armour, A. D.
name: Houzet, M.
name: Pistolesi, F.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a formalism for calculating the non-symmetrized quantum current noise within the Born-Markov approximation for the master equation. The formalism is particularly well suited to obtaining the current noise for quantum transport in mesoscopic devices such as a superconducting single electron transistor (SSET). As an example of the method, we obtain explicit results for the double Josephson-quasiparticle (DJQP) resonance in a SSET. Our calculations reveal the asymmetries that develop in the current noise as well as clarifying the behavior at high frequencies. Our findings are consistent with recent measurements of the asymmetry in the current noise spectrum.
description: 5 pages, 3 figures
Light sheet theta microscopy for rapid high-resolution imaging of large biological samples
Creators: name: Migliori, Bianca
name: Datta, Malika S.
name: Dupre, Christophe
name: Apak, Mehmet C.
name: Asano, Shoh
name: Gao, Ruixuan
name: Boyden, Edward S.
name: Hermanson, Ola
name: Yuste, Rafael
name: Tomer, Raju
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Biology
subject: Microscopy
subject: Brain--Imaging
subject: High resolution imaging
subject: Neurosciences
subject: FOS: Clinical medicine

description: Background
                Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination.

                Results
                To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality.

                Conclusions
                The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.
Atypical Integration of Sensory-to-Transmodal Functional Systems Mediates Symptom Severity in Autism
Creators: name: Park, Shinwon
name: Haak, Koen V.
name: Cho, Han Byul
name: Valk, Sofie L.
name: Bethlehem, Richard A. I.
name: Milham, Michael P.
name: Bernhardt, Boris C.
name: Di Martino, Adriana
name: Hong, Seok-Jun
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Psychiatry
autism spectrum disoder
cortical hierarchy
low-level sensory
high-order system
connectopic mapping
subcortico-cortical connectivity

description: A notable characteristic of autism spectrum disorder (ASD) is co-occurring deficits in low-level sensory processing and high-order social interaction. While there is evidence indicating detrimental cascading effects of sensory anomalies on the high-order cognitive functions in ASD, the exact pathological mechanism underlying their atypical functional interaction across the cortical hierarchy has not been systematically investigated. To address this gap, here we assessed the functional organisation of sensory and motor areas in ASD, and their relationship with subcortical and high-order trandmodal systems. In a resting-state fMRI data of 107 ASD and 113 neurotypical individuals, we applied advanced connectopic mapping to probe functional organization of primary sensory/motor areas, together with targeted seed-based intrinsic functional connectivity (iFC) analyses. In ASD, the connectopic mapping revealed topological anomalies (i.e., excessively more segregated iFC) in the motor and visual areas, the former of which patterns showed association with the symptom severity of restricted and repetitive behaviors. Moreover, the seed-based analysis found diverging patterns of ASD-related connectopathies: decreased iFCs within the sensory/motor areas but increased iFCs between sensory and subcortical structures. While decreased iFCs were also found within the higher-order functional systems, the overall proportion of this anomaly tends to increase along the level of cortical hierarchy, suggesting more dysconnectivity in the higher-order functional networks. Finally, we demonstrated that the association between low-level sensory/motor iFCs and clinical symptoms in ASD was mediated by the high-order transmodal systems, suggesting pathogenic functional interactions along the cortical hierarchy. Findings were largely replicated in the independent dataset. These results highlight that atypical integration of sensory-to-high-order systems contributes to the complex ASD symptomatology.
Inverse Ising inference using all the data
Creators: name: Aurell, Erik
name: Ekeberg, Magnus
Publisher: name: arXiv
Year: 2011
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: We show that a method based on logistic regression, using all the data, solves the inverse Ising problem far better than mean-field calculations relying only on sample pairwise correlation functions, while still computationally feasible for hundreds of nodes. The largest improvement in reconstruction occurs for strong interactions. Using two examples, a diluted Sherrington-Kirkpatrick model and a two-dimensional lattice, we also show that interaction topologies can be recovered from few samples with good accuracy and that the use of $l_1$-regularization is beneficial in this process, pushing inference abilities further into low-temperature regimes.
description: 5 pages, 2 figures. Accepted version
Additional file 1 of Sagittal intervertebral rotational motion: a deep learning-based measurement on flexion–neutral–extension cervical lateral radiographs
Creators: name: Yan, Yuting
name: Zhang, Xinsheng
name: Meng, Yu
name: Shen, Qiang
name: He, Linyang
name: Cheng, Guohua
name: Gong, Xiangyang
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified

description: Additional file 1. Percentage of correct key points (PCK) for landmarks at the 1–5-mm thresholds on flexion, neutral, and extension views.
Disease Modelling of Cognitive Outcomes and Biomarkers in the European Prevention of Alzheimer’s Dementia Longitudinal Cohort
Creators: name: Howlett, James
name: Hill, Steven M.
name: Ritchie, Craig W.
name: Tom, Brian D. M.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Big Data
Alzheimer’s disease
biomarkers
cognitive functioning
disease modelling
European prevention of Alzheimer’s dementia
latent class mixed models
precision medicine
Bayesian profile regression

description: A key challenge for the secondary prevention of Alzheimer’s dementia is the need to identify individuals early on in the disease process through sensitive cognitive tests and biomarkers. The European Prevention of Alzheimer’s Dementia (EPAD) consortium recruited participants into a longitudinal cohort study with the aim of building a readiness cohort for a proof-of-concept clinical trial and also to generate a rich longitudinal data-set for disease modelling. Data have been collected on a wide range of measurements including cognitive outcomes, neuroimaging, cerebrospinal fluid biomarkers, genetics and other clinical and environmental risk factors, and are available for 1,828 eligible participants at baseline, 1,567 at 6 months, 1,188 at one-year follow-up, 383 at 2 years, and 89 participants at three-year follow-up visit. We novelly apply state-of-the-art longitudinal modelling and risk stratification approaches to these data in order to characterise disease progression and biological heterogeneity within the cohort. Specifically, we use longitudinal class-specific mixed effects models to characterise the different clinical disease trajectories and a semi-supervised Bayesian clustering approach to explore whether participants can be stratified into homogeneous subgroups that have different patterns of cognitive functioning evolution, while also having subgroup-specific profiles in terms of baseline biomarkers and longitudinal rate of change in biomarkers.
Beyond the unitarity bound in AdS/CFT_(A)dS
Creators: name: Andrade, Tomas
name: Uhlemann, Christoph F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this work we expand on the holographic description of CFTs on de Sitter (dS) and anti-de Sitter (AdS) spacetimes and examine how violations of the unitarity bound in the boundary theory are recovered in the bulk physics. To this end we consider a Klein-Gordon field on AdS_(d+1) conformally compactified such that the boundary is (A)dS_d, and choose masses and boundary conditions such that the corresponding boundary operator violates the CFT unitarity bound. The setup in which the boundary is AdS_d exhibits a particularly interesting structure, since in this case the boundary itself has a boundary. The bulk theory turns out to crucially depend on the choice of boundary conditions on the boundary of the AdS_d slices. Our main result is that violations to the unitarity bound in CFTs on dS_d and AdS_d are reflected in the bulk through the presence of ghost excitations. In addition, analyzing the setup with AdS_d on the boundary allows us to draw conclusions on multi-layered AdS/CFT-type dualities.
description: 30 pages, 2 figures; reference added
Impediments to communication and relationships between infertility care providers and patients
Creators: name: Klitzman, Robert L.
Publisher: name: Columbia University
Year: 2018
Subjects: Physician and patient
Infertility--Patients
Patient-centered health care
Communication in medicine
Psychiatry

description: Background
                Infertility patients generally see provider-patient communication and relationships as important, but as often insufficient, raising critical questions regarding why these gaps persist, and how they might best be addressed.

                Methods
                Semi-structured interviews of approximately one hour each were conducted with 37 ART providers and patients (17 physicians, 10 other health providers, and 10 patients) and were thematically analyzed.

                Results
                Patients see clinicians’ interactions as ranging widely from good to bad, related to several specific barriers and factors. Patients and providers may differ in their physical and emotional experiences, expectations concerning treatment outcomes and uncertainties, and time frames and finances, generating dynamic processes and tensions. Characteristics of particular providers, clinics and patients can also vary. Infertility patients tend to find only one outcome acceptable – a “take home baby” – rather than partial success, as is the case with many other diseases. Yet most IVF cycles fail. Many patients must pay considerable out-of-pocket expenses for infertility treatment, exacerbating disappointments and frustrations. Providers often work in competitive, entrepreneurial markets, and “hype” their potential success. After treatment failures, providers may feel guilty and withdraw from patients. Yet these behaviors can antagonize patients more than physicians realize, aggravating patient stresses. Several providers described how they understood patients’ needs and perceptions more fully only after becoming infertility patients themselves. Interactions with not only physicians, but other providers (e.g., nurses and staff) can play key roles. Patients may be willing to understand these impediments, but providers often communicate these obstacles and reasons poorly or not at all, furthering tensions.

                Conclusions
                These data, the first to examine several critical aspects of challenges that infertility providers and patients face in communication and relationships, suggest that several key dynamic processes and factors may be involved, and need to be addressed. While prior research has shown that infertility patients value, but often feel disappointed in relationships with clinicians, the present data highlight several specific impediments, and thus have critical implications for future practice, research, guidelines and education.
title: INFECTION DYNAMICS OF MYCOPLASMA BOVIS INFECTIONS IN DAIRY HERDS
Creators: name: Biesheuvel, Marit Marleen
Publisher: name: Graduate Studies
Year: 2024
Subjects: subject: Dairy cows
subject: Mycoplasma bovis
subject: Mycoplasma spp.
subject: Infection dynamics
subject: Culture protocol
subject: Infection disease modelling
subject: Simulation
subject: Targeted enrichment
subject: Strain diversity
subject: Individual Level Model
subject: SIR
subject: Farmer behaviour
subject: Psychological Theories
subject: Surveillance
subject: Control Program
subject: Dairy herds
subject: Cattle
subject: Veterinary Science

description: Mycoplasma bovis infections affect dairy cattle worldwide, yet few countries have implemented surveillance, control, or monitoring programs. Critical gaps in understanding the disease dynamics, transmission, and epidemiology persist. Additionally, diagnosing M. bovis is challenging due to suboptimal diagnostic tests, subclinical infections and intermittent shedding, making it difficult to identify infected animals. In Chapter 2, an evidence-based evaluation of carbon dioxide (CO2) requirements in culture protocols revealed that a wider range of CO2 conditions than previously described supports M. bovis growth, and CO2 may not be necessary at all. Chapter 3 explored age-stratified transmission dynamics of M. bovis across 20 dairy farms using a Susceptible – Infected – Removed (SIR) model, discovering significant heterogeneity in basic reproduction numbers (R0) and highlighting the role of youngstock as a potential transmission reservoir. These findings were reinforced in Chapter 4, where Bayesian latent class analysis was coupled with individual level transmission modeling, which accounts for ‘prior knowledge’ on varying diagnostic test performances such as the poor sensitivity (Se) and good specificity (Sp), demonstrating improved data fit, and provided more accurate R0 estimates, though farm-to-farm variability remained. The heterogeneity observed in the transmission dynamics may be explained by strain diversity within M. bovis. In Chapter 5, a method was developed to identify strain differences. Using mock milk-samples with pure and mixed infections, and various enrichment proportions, Themisto and mSWEEP outperformed the widely used Kraken2 tool in accurately identifying M. bovis strains in silico. Enrichment of M. bovis DNA to at least 30% of the sequenced reads is enough to obtain PSV level data. Finally, Chapter 6 presents a literature review of theories and methods used to study farmer behaviour in relation to cattle disease control measures. Whereas many studies focused on personal and interpersonal factors influencing the adoption of measures, none addressed actual farmer behaviour change or broader contextual influences. A good understanding of farmers’ motivators and barriers, and what is needed to drive real change is essential before proposing any animal disease control program.