cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Modeling Human Epiblast Morphogenesis
Creators: name: Resto, Agnes
Publisher: name: My University
Year: 2023
Subjects: subject: Human embryo development
subject: Stem cell models
subject: Agent-based models
subject: Genetic algorithms
subject: Machine learning
subject: Mechanical Engineering
subject: FOS: Mechanical engineering
subject: Engineering

description: The development of the human embryo is arguably the most complex process that we could care to study. In this process, the developing embryo must undergo proliferation, reorganization, lineage diversification, and dozens of cell fate specification events. During this time, a myriad of events are happening in parallel at the cell level, each one setting the foundation for the emergence of increasingly complex tissues of increasingly complex function. Understanding the mechanisms guiding these processes is pivotal not only for embryogenesis-related applications in fertility and development, but also for regenerative medicine applications such as the development of organ replacements. In this dissertation, I propose an integrative approach to the study of morphogenesis and patterning, specifically in the context of stem cell-based models of human development. Firstly, I present a novel machine learning-assisted imaging pipeline that permits the careful characterization of cell-level events occurring in our in vitro model of epiblast cyst morphogenesis. Secondly, I present a novel agent-based model (ABM)-genetic algorithm (GA) framework for the generation of models of morphogenesis. The framework was first tested to determine its ability to generate structures of desired patterns. It was then applied for the generation of models that plausibly capture mechanisms at work during epiblast cyst morphogenesis and symmetry breaking. With preliminary in silico experiments, I showed that the framework was able to output models that partially captured the effect of initial cell number on final cyst composition. I further showed that correct structure formation was heavily impacted by just a few model parameters. Combined with in vitro experimentation, these tools have the potential to shed light into the mechanisms guiding growth, movement, and cell fate specification in in vitro models of human development.
Epidemic spreading on interconnected networks
Creators: name: Saumell-Mendiola, Anna
name: Serrano, M. Ángeles
name: Boguñá, Marián
Publisher: name: arXiv
Year: 2012
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Social and Information Networks (cs.SI)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Many real networks are not isolated from each other but form networks of networks, often interrelated in non trivial ways. Here, we analyze an epidemic spreading process taking place on top of two interconnected complex networks. We develop a heterogeneous mean field approach that allows us to calculate the conditions for the emergence of an endemic state. Interestingly, a global endemic state may arise in the coupled system even though the epidemics is not able to propagate on each network separately, and even when the number of coupling connections is small. Our analytic results are successfully confronted against large-scale numerical simulations.
The Role of the Technicians in the Digital Pathology Implementation. Searching Optimization
Creators: name: Alcaraz-Mateos, Eduardo
name: Tortosa-Martinez, I.
name: Alcolea-Guardiola, C.
name: Estevez-Ligero, S.
name: Abellan-Palazon, A.
name: Kundisova, A.
name: Nieto-Olivares, A.
name: Chaves-Benito, A.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Scanning histological or cytological preparations is a crucial element in the process of digitization of Pathology Departments, along with the traceability of tissue samples and the reports management. The scanning time and the high size of the files are still considered suboptimal for full implementation.
Aims
In order to optimize time and space a comparative study in our center has been carried out.
Methods
A total  of  25  endoscopic  samples  (5  esophageal,  5 gastric, 5 duodenal, 5 colonic inflammatory, and 5 colonic neoplastic) were selected with the intention of comparing different parameters (scanning time, error rate during scanning and hard disk storage) between the original histological glass slides (group A: 2 slides per case, 50 preparations) and new sections, with levels grouped into a single slide (group B: 1 slide per case, 25 preparations). They were scanned at 20x magnification in routine way using the Ventana iScan scanner Coreo (Roche diagnostics). The process was repeated 4 times to calculate averages.
Results
The average scanning time was 5 hours 40 minutes (6m 48s / slide) in group A and 5 hours 10 minutes (12m 24s/slide) in group B. The error rate was higher than it had been found in previous studies (2-3%) with 6% errors in group A and 3,9% errors in group B. The space occupied on the hard disk was 11.87 GB in group A and 9.6 GB in group B (475 MB/case vs 385 MB/case, respectively). The average number of tissue sections per case was 7 in group A and 8 in group B.

Conclusions: There is a clear benefit of standardizing and optimizing the number of cuts per slide in terms of storage (saving 19%), biopsy sampling (14% more tissue) and error rate (35% less), including a not negligible decrease in the scanning time (9%) in the study conducted.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Scanning tunneling spectroscopy and Dirac point resonances due to a single Co adatom on gated graphene
Creators: name: Saffarzadeh, Alireza
name: Kirczenow, George
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Based on the standard tight-binding model of the graphene $π$-band electronic structure, the extended Hückel model for the adsorbate and graphene carbon atoms, and spin splittings estimated from density functional theory (DFT), the Dirac point resonances due to a single cobalt atom on graphene are studied. The relaxed geometry of the magnetic adsorbate and the graphene is calculated using DFT. The system shows strong spin polarization in the vicinity of the graphene Dirac point energy for all values of the gate voltage, due to the spin-splitting of Co 3d orbitals. We also model the differential conductance spectra for this system that have been measured in the scanning tunneling microscopy (STM) experiments of Brar {\em et al.} [Nat. Phys. {\bf 7}, 43 (2011)]. We interpret the experimentally observed behavior of the S-peak in the STM differential conductance spectrum as evidence of tunneling between the STM tip and a cobalt-induced Dirac point resonant state of the graphene, via a Co 3d orbital. The cobalt ionization state which is determined by the energy position of the resonance can be tuned by gate voltage, similar to that seen in the experiment.
description: 12 pages, 4 figures
Geometric Manipulation of Ensembles of Atoms on Atom Chip for Quantum Computation
Creators: name: Zheng, Yicong
name: Brun, Todd A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We propose a feasible scheme to achieve quantum computation based on geometric manipulation of ensembles of atoms, and analyze it for neutral rubidium atoms magnetically trapped in planoconcave microcavities on an atom chip. The geometric operations are accomplished by optical excitation of a single atom into a Rydberg state in a constant electric field. Strong dipole-dipole interactions and incident lasers drive the dark state of the atom ensembles to undergo cyclic evolutions that realize a universal set of quantum gates. Such geometric manipulation turns out naturally to protect the qubits from the errors induced by non-uniform laser illumination as well as cavity loss. The gate performance and decoherence processes are assessed by numerical simulation.
description: 17 pages, 14 figures
Supplementary Figures and Tables from Temperature modulates immune gene expression in mosquitoes during arbovirus infection
Creators: name: B.M.C. Randika Wimalasiri-Yapa
name: Barrero, Roberto A.
name: Stassen, Liesel
name: Hafner, Louise M.
name: McGraw, Elizabeth A.
name: Pyke, Alyssa T.
name: Jansen, Cassie C.
name: Suhrbier, Andreas
name: Yakob, Laith
name: Wenbiao Hu
name: Devine, Gregor J.
name: Frentiu, Francesca D.
Publisher: name: The Royal Society
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 60408 Genomics

description: The principal vector of dengue, Zika and chikungunya viruses is the mosquito Aedes aegypti, with its ability to transmit pathogens influenced by ambient temperature. We use chikungunya virus (CHIKV) to understand how the mosquito transcriptome responds to arbovirus infection at different ambient temperatures. We exposed CHIKV-infected mosquitoes to 18, 28 and 32°C and found that higher temperature correlated with higher virus levels, particularly at 3 days post infection, but lower temperature resulted in reduced virus levels. RNAseq analysis indicated significantly altered gene expression levels in CHIKV infection. The highest number of significantly differentially expressed genes was observed at 28°C, with a more muted effect at the other temperatures. At the higher temperature, the expression of many classical immune genes, including Dicer-2, was not substantially altered in response to CHIKV. The upregulation of Toll, IMD and JAK-STAT pathways was only observed at 28°C. Functional annotations suggested that genes in immune response and metabolic pathways related to energy supply and DNA replication were involved in temperature-dependent changes. Time post infection also led to substantially different gene expression profiles, and this varied with temperature. In conclusion, temperature significantly modulates mosquito gene expression in response to infection, potentially leading to impairment of immune defences at higher temperatures.
Primordial non-Gaussianity from mixed inflaton-curvaton perturbations
Creators: name: Fonseca, José
name: Wands, David
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We characterise the primordial perturbations produced due to both inflaton and curvaton fluctuations in models where the curvaton has a quadratic, cosine or hyperbolic potential, and the inflaton potential is characterised by the usual slow-roll parameters. Isocurvature curvaton field perturbations can produce significant non-Gaussianity in the primordial density field, in contrast with adiabatic inflaton field perturbations which produce negligible non-Gaussianity for canonical scalar fields. A non-self-interacting curvaton with quadratic potential produces a local-type non-Gaussianity that is well described by the non-linearity parameter fNL, which may be scale-dependent when the inflaton perturbations dominate the power spectrum. We show how observational bounds on non-linearity parameters and the tensor-scalar ratio can be used to constrain curvaton and inflaton parameters. We find a consistency relation between the bispectrum and trispectrum parameters in a mixed inflaton-curvaton model for a quadratic curvaton potential. Self-interaction terms in the curvaton potential can lead to both a large trispectrum parameter, gNL, and scale-dependence of the non-linearity parameters.
description: 17 pages, 8 figures, (v2 references added)
Novel Whiffling-Inspired Gapped Wings as Control Surfaces
Creators: name: Sigrest, Piper
Publisher: name: My University
Year: 2023
Subjects: subject: whiffling
subject: bioinspiration
subject: control surface
subject: UAV
subject: avian
subject: Aerospace Engineering
subject: FOS: Mechanical engineering
subject: Engineering

description: Some bird species fly inverted (“whiffle”) to lose altitude, move laterally, and respond to gusts. Inverted flight twists the primary feathers, creating gaps along the trailing edge and decreasing lift. Whiffling shares parallels to conventional spoilers and ailerons on uncrewed aerial vehicles (UAVs). However, the maneuver had yet to inspire aircraft design. Here, I investigate the capabilities of a novel UAV control surface − a wing with gaps in the trailing edge − using the feather rotation mechanism as a new source of bio-inspiration. Wind tunnel tests revealed that the gapped wings did not reduce lift as much as a spoiler. However, at high angles of attack, a gapped wing produced a greater rolling moment coefficients than a maximum-deflected single aileron. I then simulated a gapped wing with a commercial computational fluid dynamics solver to estimate its work requirements. The gapped wing required higher work than a single aileron at low rolling moment coefficients. However, the gapped wing required less work at higher rolling moment coefficients and ultimately produced a higher maximum rolling moment coefficient. The results also highlighted the fluid dynamics mechanisms underlying the behavior the gapped wings. I additionally compared the gapped wing to a realistic wing with two ailerons. Compared to the two-aileron wing, the gapped wing produced smaller rolling moment coefficients, but favorable yaw at low rolling moment coefficients. A parameter sweep of gap size and configuration further implied that gap geometry could be tailored to maximize rolling moment coefficient per actuation work. Finally, I analytically modelled the rigid body dynamics of aircraft with varying gapped wings. The gaps generally improved the longitudinal modes. They also effectively damped and reduced the amplitude of the gust response. Ultimately, despite several limitations, the gapped wings could be a useful gust mitigation or roll control surface in certain situations.
title: Unconventional credit policy in an economy under zero lower bound
Creators: name: Pozo, Jorge
name: Rojas, Youel
Publisher: name: Graduate Institute of International and Development Studies
publisherIdentifier: https://ror.org/007ygn379
publisherIdentifierScheme: ROR
Year: 2021

description: Graduate Institute of International and Development Studies Working Paper ; no. 14/2021
The Impact Of Introducing Virtual Slides As A Replacement For Powerpoint Presentations In The Students’ Microscopy Labs
Creators: name: Vaduva, Adrian
name: Cornea, R.
name: Cornianu, M.
name: Mihai, I.
name: Muresan, A.
name: Vita, O.
name: Derban, M.
name: Jurescu, A.
name: Gheju, A.
name: Taban, S.
name: Lazureanu, C.
name: Duta, C.
name: Lazar, F.
name: Dema, A.
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
The medical school students in Timisoara, Romania have been studying pathology slides in microscopy labs according to a protocol which uses classical PowerrPoint presentations as guides for understanding the microscopic features of diseases, followed by individual examination of the glass slides under the microscope.
Aims
We aimed to assess the impact of replacing those presentations with virtual slides (VS).
Methods
In the middle of the semester, for the benign tumors microscopy lab, which is presented over the course of 2 weeks, we used 3 VS, while the other 3 slides were presented in the classical PowerPoint manner. All attending students from the 3rd year of the Medical School of the University of Medicine and Pharmacy “Victor Babes” Timisoara were asked to fill out an anonymous questionnaire at the end of the lab, in which they graded the difficulty in identifying lesions, chose the best/least understood lesion and pointed out the best manner of presentation.
Results
431 valid questionnaires were collected. 52.9% of the students indicated one of the 3 VS as the best understood lesion, while 59.62% chose a different VS as a least understood one. One VS was also the top best (113/332 votes) while another the least understood (34/126 votes) lesion. 74.01% students agreed that VS helped them understand the microscopic criteria better, while 74.71% would like VS to be used in the labs to come.

Conclusion: VS were appreciated by the students as a novelty and a more impressing way of studying pathology slides, but did not dramatically improve the easiness with which they identify and understand the lesions.

Work supported by the project „Studiu multicentric privind utilizarea abordului robotic în corelarea scăderii nivelului de adipokine circulante din obezitate cu riscul apariţiei cancerului pelvin < ROBOCAPE >” - ID 1846 / Cod SMIS 48478 - POSCCE
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Mexican private higher education : the potential of private and public goods
Creators: name: Prieto, Carlos
Publisher: name: University of British Columbia
Year: 2010

description: In this qualitative case study, I explore the organizational processes and policy discourses at one private higher education institution in Mexico. By using a theoretical framework relative to contestations between the global “ideology of privatization” in education (Rizvi, 2006; Rizvi & Lingard, 2009) and the “global public good” of private education (Marginson, 2007; Menashy, 2009), I examine how external forces are influencing a private institution and its opportunities relative to the public/private good. The study provides answers to three main research questions: 1. What are the assumptions, beliefs and knowledge of upper level management of the private education institution with regard to the global and local forces (economic, political, technological, and social) that influence the organization and its opportunities? 2. What are the assumptions, beliefs and knowledge of upper level management in internal processes in response to external pressures relative to the provision of public versus private goods? 3. How does the institution position itself relative to other educational opportunities (public and private) at the local, national, and global levels? The study was undertaken at an established private business school in Mexico. Data collection took place from February through April 2010 using a strategic sample of participants (men and women) with high-level positions in the school. The study consisted of semi structured interviews, which were digitally recorded and subsequently transcribed, coded, and analyzed thematically. The findings of this study reveal interesting issues and processes of the social imaginary of senior level executives related to neoliberal discourses, predominantly in relation to the effects of competition in higher education. Particular attention is paid to the institution’s potential to generate public and private goods, and to the value of positional goods relative to other educational opportunities (public and private) at the local, national and global levels.
Cluster formation and evolution in networks of financial market indices
Creators: name: Junior, Leonidas Sandoval
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistical Finance (q-fin.ST)
subject: FOS: Economics and business

description: Using data from world stock exchange indices prior to and during periods of global financial crises, clusters and networks of indices are built for different thresholds and diverse periods of time, so that it is then possible to analyze how clusters are formed according to correlations among indices and how they evolve in time, particularly during times of financial crises. Further analysis is made on the eigenvectors corresponding to the second highest eigenvalues of the correlation matrices, revealing a structure peculiar to markets that operate in different time zones.
Figures S1 - S3 from Bringing the Ca2+-sensitivity of myristoylated recoverin into the physiological range
Creators: name: Marino, Valerio
name: Riva, Matteo
name: Zamboni, Davide
name: Karl-Wilhelm Koch
name: Dell'Orco, Daniele
Publisher: name: The Royal Society
Year: 2020
Subjects: Biophysics
Biochemistry
Neuroscience
Structural Biology

description: Figure S1: A) Far UV CD spectra of 10 µM nmRec and 300 µM EGTA (black), after sequential additions of 1 mM free Ca2+ (red), 15 µM GRK1 peptide (blue) and 4.2 mM free EGTA (green). B) Far UV CD spectra of 10 µM nmRec and 300 µM EGTA (black), after sequential additions of 15 µM GRK1 peptide (red), 1 mM free Ca2+ (blue) and 4.2 mM free EGTA (green). C) Far UV CD spectra of 10 µM mRec and 300 µM EGTA (black), after sequential additions of 1 mM free Ca2+ (red), 15 µM GRK1 peptide (blue) and 4.2 mM free EGTA (green). D) Far UV CD spectra of 10 µM mRec and 300 µM EGTA (black), after sequential additions of 15 µM GRK1 peptide (red), 1 mM free Ca2+ (blue) and 4.2 mM free EGTA (green).; Figure S2: Hydrodynamic diameter estimation of 15 nM LP monitored by A) DLS and B) Nanoparticle Tracking Analysis.; Figure S3: Near UV CD spectra of 7 µM mRec in the presence of 5 nM LP and 300 µM EGTA (black) or 1 mM Ca2+ (red). B) Near UV CD spectra of 7 µM mRec in the presence of 5 nM LP, 10.5 µM GRK1 peptide and 300 µM EGTA (black) or 1 mM Ca2+.
A non-local inequality and global existence
Creators: name: Gressman, Philip T.
name: Krieger, Joachim
name: Strain, Robert M.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Analysis of PDEs (math.AP)
subject: Mathematical Physics (math-ph)
subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: In this article we prove a collection of new non-linear and non-local integral inequalities. As an example for $u\ge 0$ and $p\in (0,\infty)$ we obtain $$ \int_{\threed} dx ~ u^{p+1}(x) \le (\frac{p+1}{p})^2 \int_{\threed} dx ~ \{(-\triangle)^{-1} u(x) \} \nsm \nabla u^{\frac{p}{2}}(x)\nsm^2. $$ We use these inequalities to deduce global existence of solutions to a non-local heat equation with a quadratic non-linearity for large radial monotonic positive initial conditions. Specifically, we improve \cite{ksLM} to include all $α\in (0, 74/75)$.
description: 6 pages, to appear in Advances in Mathematics
Independent electrical tuning of separated quantum dots in coupled photonic crystal cavities
Creators: name: Thon, Susanna M.
name: Kim, Hyochul
name: Bonato, Cristian
name: Gudat, Jan
name: Hagemeier, Jenna
name: Petroff, Pierre M.
name: Bouwmeester, Dirk
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Systems of photonic crystal cavities coupled to quantum dots are a promising architecture for quantum networking and quantum simulators. The ability to independently tune the frequencies of laterally separated quantum dots is a crucial component of such a scheme. Here, we demonstrate independent tuning of laterally separated quantum dots in photonic crystal cavities coupled by in-plane waveguides by implanting lines of protons which serve to electrically isolate different sections of a diode structure.
description: 3 pages, 3 figures
Forecasting Electric Vehicle Charging Behavior in Workplace Charging Infrastructure with Limited Privacy-Restricted Real Data
Creators: name: Stein, Alexander
name: Beichter, Sebastian
name: Hage, Jacek
name: Beichter, Maximilian
name: Schwarz, Bernhard
name: Waczowicz, Simon
name: Hiller, Marc
name: Hagenmeyer, Veit
name: Munzke, Nina
name: Mikut, Ralf
Publisher: name: Institute of Electrical and Electronics Engineers (IEEE)
Year: 2024

description: Workplace Charging Stations (CSs) are well-suited to improve grid stability by scheduling the charging process over the parking duration and thereby reducing the peak load. Therefore, the energy demand and parking duration of single charging sessions must be known as well as the future occupancy of the CS. Since user IDs are often unknown for privacy reasons, this paper investigates how these parameters can be predicted for future charging events. The charging behavior is examined for its characteristic features, such as location, arrival, and departure times. First, calendar, weather, lag and CS-specific features are implemented and used to train nine different machine-learning algorithms. For the observed data, the Random Forest Regressor yields the best results for parking duration and energy demand. For parking duration, a 33.7% improvement in Mean Absolute Percentage Error (MAPE) over the baseline (the mean parking duration) can be achieved. The MAPE of the parking duration forecast is 71.0% and for the energy demand, it is 84.0% which leads to the conclusion that without the knowledge of user IDs predicting the charging behavior of users is possible only to a limited extent.
Single-photon nonlinear optics with Kerr-type nanostructured materials
Creators: name: Ferretti, Sara
name: Gerace, Dario
Publisher: name: arXiv
Year: 2012
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We employ a quantum theory of the nonlinear optical response from an actual solid-state material possessing an intrinsic bulk contribution to the third-order nonlinear susceptibility (Kerr-type nonlinearity), which can be arbitrarily nanostructured to achieve diffraction-limited electromagnetic field confinement. By calculating the zero-time delay second-order correlation of the cavity field, we set the conditions for using semiconductor or insulating materials with near-infrared energy gaps as efficient means to obtain single-photon nonlinear behavior in prospective solid-state integrated devices, alternative to ideal sources of quantum radiation such as, e.g., single two-level emitters.
description: 5 pages, three figures
Antiferromagnetic Order and Superconductivity in Sr4(Mg0.5-xTi0.5+x)2O6Fe2As2 with Electron Doping: 75As-NMR Study
Creators: name: Yamamoto, Keisuke
name: Mukuda, Hidekazu
name: Kinouchi, Hiroaki
name: Yashima, Mitsuharu
name: Kitaoka, Yoshio
name: Yogi, Mamoru
name: Sato, Shinya
name: Ogino, Hiraku
name: Shimoyama, Jun-ichi
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We report an 75As-NMR study on iron (Fe)-based superconductors with thick perovskitetype blocking layers Sr4(Mg0.5-xTi0.5+x)2O6Fe2As2 with x=0 and 0.2. We have found that antiferromagnetic (AFM) order takes place when x=0, and superconductivity (SC) emerges below Tc=36 K when x=0.2. These results reveal that the Fe-pnictides with thick perovskitetype blocks also undergo an evolution from the AFM order to the SC by doping electron carriers into FeAs planes through the chemical substitution of Ti+4 ions for Mg+2 ions, analogous to the F-substitution in LaFeAsO compound. The reason why the Tc=36 K when x=0.2 being higher than the optimally electron-doped LaFeAsO with Tc=27 K relates to the fact that the local tetrahedron structure of FeAs4 is optimized for the onset of SC.
description: 4 pages, 3 figures, 1 table
Novel anti-human Axl monoclonal antibodies for improved patient biomarker studies
Creators: name: Ahmed, Lavina
name: Kiprijanov, Sergej M
name: Nalwoga, Hawa
name: Wnuk-Lipinska, Katarzyna
name: Haugen, Hallvard
name: Lorens, James B
name: Akslen, Lars A
name: Micklem, David Robert
Publisher: name: Diagnostic Pathology
Year: 2016
Subjects: Monoclonal antibodies; cancer; EMT; diagnostic biomarkers; Axl; ELISA; IHC; Western blot

description: Background: Axl receptor tyrosine kinase has been associated with poor clinical outcome in a wide variety of malignancies including breast, lung, prostate, pancreatic, brain and myeloid cancers. Axl is up-regulated during tumour epithelial-to-mesenchymal transition (EMT) and is associated with metastasis, immune evasion and drug resistance.

Methods: The aim of this study was to develop improved assays for detection of Axl protein in patient samples. We developed a panel of mouse monoclonal antibodies directed against the extracellular domain of human Axl, from mice immunized with a recombinant antigen comprising the extracellular domains of human Axl fused to human IgG1 Fc domain. Anti-Axl monoclonal antibodies (MAbs) were assessed for sensitivity, specificity and utility using surface plasmon resonance (SPR) analysis, sandwich enzyme-linked immunosorbent assay (ELISA), Western blot analysis and immunohistochemistry (IHC) staining.

Results: One of the anti-human Axl MAb,1H12, performed particularly well, and SPR analysis confirmed both high affinity (50 pM) and high selectivity for Axl versus other Axl-family receptors. In IHC applications on selected human carcinomas and cancer cell line pellets, MAb 1H12 showed improved sensitivity and reduced background staining compared to other members of the MAb panel. A second MAb 5F11 showed very high affinity (5.8 pM) at a non-overlapping epitope and was selected as a partner for 1H12 in sandwich ELISA, producing a highly sensitive and specific assay.
Conclusion: MAbs 1H12 and 5F11 represent new anti-human Axl monoclonal antibodies for improved patient biomarker studies.
description: Diagnostic Pathology, Vol 2 No 1 (2016): 2016
Optical spectroscopy of the quiescent counterpart to EXO 0748-676: a Black Widow scenario?
Creators: name: Ratti, E. M.
name: Steeghs, D. T. H.
name: Jonker, P. G.
name: Torres, M. A. P.
name: Bassa, C. G.
name: Verbunt, F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present phase-resolved optical spectroscopy of the counterpart to the neutron star low mass X-ray binary EXO 0748-676, almost one year after it turned into quiescence. The spectra display prominent Hbeta and Hgamma and weak Fe II lines in emission. An average of all the spectra (corrected for the orbital motion) also exhibits a very weak line from Mg I. Tomographic reconstructions show that the accretion disc is not contributing to the optical line emission, which is instead dominated by the irradiated hemisphere of the companion star facing the neutron star. We could not detect absorption features from the mass donor star in the spectra. The emission lines appear broad, with an intrinsic FWHM of 255+-22 km/s. Under the assumption that the width of the Fe II emission lines is dominated by rotational broadening, we obtain a lower limit on the compact object mass which is inconsistent with a NS accretor. We discuss this incongruity and conclude that either the lines are blends of unresolved features (although this requires some fine tuning) or they are broadened by additional effects such as bulk gas motion in an outflow. The fact that the Fe II lines slightly lag in phase with respect to the companion star can be understood as outflowing gas consistent with a Black-Widow like scenario. Nevertheless, we can not rule out the possibility that blends of various emission lines cause the apparent phase lag of the Fe II emission lines as well as their large width.
description: 10 pages,5 figures. Accepted for publication in MNRAS
Entanglement and Extreme Spin Squeezing for a Fluctuating Number of Indistinguishable Particles
Creators: name: Hyllus, Philipp
name: Pezze, Luca
name: Smerzi, Augusto
name: Toth, Geza
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We extend the criteria for $k$-particle entanglement from the spin squeezing parameter presented in [A.S. Sørensen and K. Mølmer, Phys. Rev. Lett. {\bf 86}, 4431 (2001)] to systems with a fluctating number of particles. We also discuss how other spin squeezing inequalities can be generalized to this situation. Further, we give an operational meaning to the bounds for cases where the individual particles cannot be addressed. As a by-product, this allows us to show that in spin squeezing experiments with cold gases the particles are typically distinguishable in practise. Our results justify the application of the Sørensen-Mølmer bounds in recent experiments on spin squeezing in Bose-Einstein condensates.
Versatile helimagnetic phases under magnetic fields in cubic perovskite SrFeO3
Creators: name: Ishiwata, S.
name: Tokunaga, M.
name: Kaneko, Y.
name: Okuyama, D.
name: Tokunaga, Y.
name: Wakimoto, S.
name: Kakurai, K.
name: Arima, T.
name: Taguchi, Y.
name: Tokura, Y.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A helical spin texture is of great current interest for a host of novel spin-dependent transport phenomena. We report a rich variety of nontrivial, helimagnetic phases in the simple cubic perovskite SrFeO3 under magnetic fields up to 42 T. Magnetic and resistivity measurements revealed that the proper-screw spin phase proposed for SrFeO3 can be subdivided into at least five kinds of ordered phases. Near the multicritical point, an unconventional anomalous Hall effect was found to show up and was interpreted as due to a possible long-period noncoplanar spin texture with scalar spin chirality.
description: 5 pages, 5 figures, Physical Review B in press
Contribution of Measurement to morphologic Diagnostics
Creators: name: Kayser, Klaus
name: Borkenfeld, Stephan
name: Carvalho, Rita
name: Kayser, Gian
Publisher: name: Diagnostic Pathology
Year: 2016
Subjects: interactive publication ;Morphological diagnostics; epistemological; methodological; individual; communicative; economical and ethical limits

description: Interactive contribution:

Pathologists' diagnostics are based upon morphology, which means to distinguish between structure and function. Morphology is the evaluation of biological structures. These are ordered clusters of material (genes, nuclei, cells, organs, etc.) that remain constant during the period of detection and observation. The observation time is an important factor that defines biological structures and diagnostics too. The implementation of measurement - based diagnostic algorithms improves the accuracy and serves for quality assurance in tissue - based diagnosis.
description: Diagnostic Pathology, Vol 2 No 1 (2016): 2016
Query Expansion: Term Selection using the EWC Semantic Relatedness Measure
Creators: name: Klyuev, Vitaly
name: Haralambous, Yannis
Publisher: name: arXiv
Year: 2011
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: This paper investigates the efficiency of the EWC semantic relatedness measure in an ad-hoc retrieval task. This measure combines the Wikipedia-based Explicit Semantic Analysis measure, the WordNet path measure and the mixed collocation index. In the experiments, the open source search engine Terrier was utilised as a tool to index and retrieve data. The proposed technique was tested on the NTCIR data collection. The experiments demonstrated promising results.
description: 5 pages, 1 figure, accepted at ASIR'11
Open Access Publication In Pathology – Advantages, Constraints And New Tools
Creators: name: Carvalho, Rita
name: Borkenfeld, Stephan
name: Kayser, Klaus
Publisher: name: Diagnostic Pathology
Year: 2016

description: Introduction/ Background
Open access journals are financed by authors (i.e. re- search grants), rather than by readers or subscribers. This business model allows a world – wide uncontrolled distribution of medical information and scientific knowledge. The financial of shifting the finance and the opportunities for misuse raise significant concerns regarding non – scientific impact and article content integrity.
Aims
Herein we report and discuss ideas and experiences of open access publication focusing on diagnostic pathology.
Methods
Our experiences are drawn from the open access online journal diagnosticpathology.eu. The journal offers the opportunity to publish case reports “beside the microscope” and to submit data for “interactive publication”. Both tools are unique, and cannot be found elsewhere. For publication of suitable articles, we demand the submission of glass slides, which will become completely digitized (virtual slides, VS).
Results
The journal is online since ten months, and the only completely independent open access journal in medicine. We have published several case reports under the headline “How do I diagnose…?” The presented form offers a guide through the article and permits a complete publication “besides the microscope”, commonly in less than one hour. Automated links to reference search items are included as well as virtual slides. The strict publication format permits fast submission of unique or interesting cases, and, in addition, the implementation of the publication into a case – related open and flexible image date bank.

 Conclusions

The mandatory inclusion of virtual slides is a unique quality control. The journal diagnosticpathology. eu is embedded in a cloud that will consist of an archive of published cases with virtual slides, an express review forum with a corresponding duty plan, an automated measurement system of histological slides, and open access atlases such as hazards of natural and artificial fibers (fine granulate)  and a  collection of  all known pulmonary diseases.
Acknowledgement
The financial support of the Verein zur Förderung des biologisch - technologischen Fortschritts in der Medizn e. V. is gratefully acknowledged.
description: Diagnostic Pathology, Vol 1 No 8 (2016): 13. European Congress on Digital Pathology
Four-body resonances of 7B using the complex scaling method
Creators: name: Myo, Takayuki
name: Kikuchi, Yuma
name: Kato, Kiyoshi
Publisher: name: arXiv
Year: 2011
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: We study the resonance spectroscopy of the proton-rich nucleus 7B in the 4He+p+p+p cluster model. Many-body resonances are treated on the correct boundary condition as the Gamow states using the complex scaling method. We predict five resonances of 7B and evaluate the spectroscopic factors of the 6Be-p components. The importance of the 6Be(2+)-p component is shown in several states of 7B, which is a common feature of 7He, a mirror nucleus of 7B. For only the ground state of 7B, the mixing of 6Be(2+) state is larger than that of 6He(2+) in 7He, which indicates the breaking of the mirror symmetry. This is caused by the small energy difference between 7B and the excited 6Be(2+) state, whose origin is the Coulomb repulsion.
description: 10 pages, 7 figures
Identities in ink: exploring connections between tattoos and ethnic identities in the ancient Nile Valley
Creators: name: Kay, Michelle
Publisher: name: Macquarie University
Year: 2023
Subjects: Other education not elsewhere classified

description: Tattooing has been practiced throughout human history using different methods and for many, culturally specific, purposes. Studying tattoos from archaeological contexts provides an opportunity to access the cultural practices that might be connected to tattooing, in particular the complex social messages conveyed by tattoos within and between groups. This thesis reviews the archaeological evidence for tattooing practices in the ancient Nile Valley to investigate their possible connections to ethnicity. The scope of this study includes known tattooed human remains and material culture related to the practice of tattooing from the regions of Egypt and Lower Nubia from the mouth of the Delta to the site of Kerma. It includes the Egyptian Predynastic Period to the New Kingdom (5300–1069 BCE), and temporally encompasses the Nubian A-Group, C-Group, Pan-Grave, and Kerma cultures. At the core of this project is a case study of three women with tattoos, uncovered during excavations at the mortuary temple of Mentuhotep II at Deir el Bahari, Egypt, in 1891 and 1923. These individuals have been understudied thus far and interpretations of them are controversial, with the primary point of contention being their supposed ethnicities. Can they be identified as Nubian or Egyptian, and how might their tattoos inform our discussions and interpretations? This case study speaks to broader questions in the scholarship regarding if, and how, tattoos might have been specific to certain cultures or ethnic groups and functioned as markers of ethnicity in the ancient Nile Valley. Overall, this research problematises the simplistic correlation of tattooing styles with dichotomic constructions of ‘Egyptian’ and ‘Nubian’ ethnicities. Future research on this topic might investigate how other aspects of identity including gender, age, status, and familial links are connected to tattooing in intersection with ethnic identities.
AudiAnnotate Audiovisual Extensible Workflow (AWE) Survey Results
Creators: name: Clement, Tanya
Publisher: name: The University of Texas at Austin
Year: 2021
Subjects: Annotation, Digital Humanities, Sound Studies, Preservation and Access

description: This survey was produced as part of the Andrew W. Mellon-funded AudiAnnotate Audiovisual Extensible Workflow (AWE)1 project in order to better understand how and why students, teachers, information professionals, and others annotate audiovisual content. It is clear from the participant responses that there is an active community annotating audiovisual content for a variety of reasons, using a variety of tools. The survey confirms and further informs the project team’s understanding of the current audiovisual annotation landscape and supports the grant’s premise that there is a broad need for a workflow that supports collaborative editing, flexible modes of presentation, and permissions control. To support these needs, the AudiAnnotate project is developing AWE, a documented workflow using the recently adopted IIIF standard for audiovisual materials that will help libraries, archives, and museums (LAMs), scholars, and the public find, access and use audiovisual cultural heritage items.
RIGHTS OF NATURE FRAMEWORK AN APPROACH TOWARDS PROMOTING ECOSYSTEM PROTECTION AND RESTORATION IN THE PHILIPPINES
Creators: name: Sadiwa, Malaya
Publisher: name: Zenodo
Year: 2023

description: This paper aims to present and introduce the Rights of Nature concept as a growing global framework movement that seeks to protect the environment by recognizing that nature, particularly ecosystems, like humans, have intrinsic rights to live.
The Rights of Nature framework acknowledges that ecosystems and natural communities are not mere assets subject to ownership; instead, they are living entities with an inherent and unassailable right to thrive and endure. Its mission is to promote the preservation and revitalization of ecosystems.
As of 2022, 24 countries, including Colombia, New Zealand, Bangladesh, Australia, India, seven Tribal Nations in the U.S. and Canada, and over 60 U.S. cities and counties, have introduced laws recognizing nature's rights. In various parts of the world, local and national courts have granted ecosystems the status of living beings and, in some cases, personhood. New laws are continuously being developed to regulate and protect the natural environment. These laws have changed how we view ecosystems and natural communities, giving them rights that can be enforced by people, governments, and communities working to benefit nature.
In 2018, the Rights of Nature have been adopted in the Philippines. It is now a growing movement in the Philippines, and they are also pushing for a bill called the Rights of Nature Act 2022 that aims to protect the country's ecosystems by giving legal personhood to nature.
Dynamics of multi-modes maximum entangled coherent state over amplitude damping channel
Creators: name: Allati, A. El
name: Hassouni, Y.
name: Metwally, N.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The dynamics of maximum entangled coherent state travels through an amplitude damping channel is investigated. For small values of the transmissivity rate the travelling state is very fragile to this noise channel, where it suffers from the phase flip error with high probability. The entanglement decays smoothly for larger values of the transmissivity rate and speedily for smaller values of this rate. As the number of modes increases, the travelling state over this noise channel loses its entanglement hastily. The odd and even states vanish at the same value of the field intensity.
Learning to be a mother, to be a mother learning, a mother learning to be
Creators: name: Lee, Fiona Ruth Grace
Publisher: name: University of British Columbia
Year: 2010

description: Adult learning is “a multidimensional phenomenon ... that takes place in various contexts”, including those that are concurrently individual, familial, and societal (Merriam 2008, p. 97). Through a process that is located, dynamic, informal and formal, and occurs in both public and private contexts, this thesis employs autobiographical bricolage to articulate my mother learning in a rich, layered exploration and expression of insights. Over the course of my writings, I explored my identity, role, and practices within the contexts of family relationships, communities of peers and mentors, and the wider North American context. Through this method, I articulate the spectrum of mental, emotional, psychological, relational, spiritual, embodied, and artistic learning in which I have been engaged, while also locating my self in the context of the broader educational and interdisciplinary discussions on mothering and learning. This thesis gives shape to my mother learning journey: a process of identification and reflection which grants me insight into other parents’ ways of “knowing, learning, and being” and has fostered in me the desire to facilitate and provide compassionate support for other parent learners (Grumet 1988, p. 149; Holman-Jones 2008, p. 209; Geertz 2003, p. 149). This desire to develop “a shared consciousness” is rooted in a desire to foster the “surprising insights” that Davis, et al. (2000) claim will inspire learners to continue seeking growth and challenge (Clarke & Collins 2007, p. 167; p. 148). Self-exploration informs my role as a parent educator seeking to enrich the mutual learning of parent-learners and educators. Through clarification of the mother learning of my predecessors and by offering new “methods and meaning”, I hope to incite change through a process which layers cycles of reflection and re-imagining (Byrne-Armstrong 2001, p. 72; Grumet 1988, p. 90, 93, 19; Holman-Jones 2003, p. 111). My own transformation from an isolated, fearful, and discouraged woman who felt constrained by her mother role, to that of a layered, humbled, questioning, and resourceful mother, daughter, wife, and educator define the borders of this thesis, but not of my learning journey as a mother and parent educator. This journey continues still now.
SUPER MOONS, COVID-19, AND QURAN: FINAL OBSERVATIONS
Creators: name: khodadoost, baback
Publisher: name: Zenodo
Year: 2023

description: ABSTRACT
Statistics of the Covid-19 pandemic show unique coincidences of prominent pandemic events with Super Moon occurrences. Although no causal relation can be suggested for these coincidences, they are interesting insofar as they may be linked to possible futuristic messages embedded in the Quran. Newly observed Super Moon coincidences, along with those observed before, could further support a pandemic perspective for chapter 74 in the Quran. This article presents the final observations related to this general topic and is complementary to the two other articles published before.