cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Localized juvenile spongiotic gingival hyperplasia in adults; investigation of possible viral etiology and comparison with pyogenic granuloma
Creators: name: Mora-Gonzalez, Danny
Publisher: name: University of North Carolina at Chapel Hill
Year: 2014

description: Localized Juvenile Spongiotic Gingival Hyperplasia (LJSGH) has been recognized in adults in our laboratory. This study reports histopathologic and clinical findings in a group of adults with lesions identical to those in LJSGH and offers evidence for change in nomenclature. This retrospective study reviewed cases histopathologically diagnosed as pyogenic granuloma of the gingiva in patients over age 21 to determine the incidence of LJSGH in the adult population. qRT-PCR for detection of possible viral etiology was done for Human papillomavirus, Human hespesvirus and Human polyomavirus. Of the cases that qualified for review, 19 within an age range 21-84 met the histopathologic criteria previously reported for LJSGH. Additionally, previously unreported presence of eosinophils and mast cells were observed. We report 19 cases of LJSGH in adults similar to the cases previously reported in pediatric population. Therefore, we propose a modification of the name to localized spongiotic gingival hyperplasia (LSGH) so that the lesion can be recognized and studied in both populations. DNA was extracted from formalin fixed, paraffin embedded, tissue sections and was examined for the detection of HPV, HHV and Polyomavirus by Real Time PCR. Our findings also suggest investigation of hypersensitivity as a possible etiologic factor.
BioExcel Deliverable D1.5 - Final project release of pilot applications
Creators: name: Abraham, Mark
name: Ippoliti, Emiliano
name: Trellet, Mikael
name: Bonvin, Alexandre
name: Gapsys, Vytautas
name: de Groot, Bert
name: Soiland-Reyes, Stian
Publisher: name: Zenodo
Year: 2018

description: This document describes the contents of the final project release of software developed for pilot applications in BioExcel. The efforts of Work Package 1 are spread over the entire project timeframe, and some collaborations, previous deployments and benchmarks have also used preliminary new code. However, to provide reference versions of all codes used in the project (e.g. to integrate them in BioExcel workflows and facilitate use by other BioExcel teams), the Work Package also makes these formal code releases. This also comes with records describing the current status of the software that results from the planning, development, documentation, and testing processes described in Deliverable 1.1 (10.5281/zenodo.263908) and the BioExcel white paper on scientific software engineering (10.5281/zenodo.1194634). The release itself takes the form of a package of Open Source-licensed source code, containing the newly developed task-parallel and throughput-oriented modules, and can be downloaded from the BioExcel webpage at http://bioexcel.eu/software/code-repositories, or from the permanent repository at (10.5281/zenodo.1473685). For most of the codes this is a BioExcel- specific repository to sync the releases with other project needs, while general users are usually recommended to follow the documentation, download and installation instructions available on the main application web pages. This release updates the previous project release reported in Deliverable 1.2 (10.5281/zenodo.574459).
Lessons in leadership: learning from teacher leaders
Creators: name: Hart, Catherine Pendleton
Publisher: name: University of North Carolina at Chapel Hill
Year: 2010

description: This paper is based on a study intended to define and explore teacher leadership from the teachers' point-of-view to help us consider what paths school systems, universities, and policy makers might take to support the development of teacher leaders who can transform schools through and beyond their classrooms. The significance of teacher leaders on the achievement and development of students is well-documented, but without a stronger research base from which to understand how teachers become teacher leaders and enact leadership, we will limit our efforts to help teachers better shape the policies and practices that determine students' experiences. This paper discusses the findings from interviews with five self-identified teacher leaders and suggests recommendations for changes to support further development of teacher leaders.
BioExcel-2 Deliverable 6.3 – High Performance Computing in support of COVID-19 Research
Creators: name: Apostolov, Rossen
name: Bonvin, Alexandre
name: Morozov, Dmitry
name: Soiland-Reyes, Stian
name: Hospital, Adam
name: De Groot, Bert
Publisher: name: Zenodo
Year: 2021

description: The unexpected emergence and spread of the SARS-CoV-2 virus and COVID-19 disease had a dramatic impact on societies across the world. Very soon it became clear that concerted efforts are needed in the fight against the pandemic. As a focal point for the computational biomolecular research communities in Europe, BioExcel restructured its efforts in support of addressing the crisis. We developed and launched a number of portals for COVID-19 related data management and analysis. High-priority access to compute resources was provided by partner HPC centers. We started numerous collaborative research projects including close partnerships with pharma industry. Community support was extended. We participated in dedicated webinars and presentations to cover methodologies, experience and results from our work. We added a dedicated section to our website under category Research (https://bioexcel.eu/covid-19-research/) to present the various services and activities related to the disease. In this document we summarize the aforementioned activities.
description: Deliverable will be published after it is accepted by the funding agency.
M3.2 - Proposal for an EOSC PID Service providers coordination mechanism
Creators: name: Mejias, Gabriela
name: Cousijn, Helena
name: Marjamaa-Mankinen, Liisa
name: Nordling, Josefine
name: van Lieshout, Natascha
name: Gonzalez-Beltran, Alejandra
Publisher: name: Zenodo
Year: 2023
Subjects: FAIR
FAIR data
FAIR-IMPACT
PIDs
persistent identifiers

description: Persistent identifiers (PIDs) are crucial to enable and achieve the FAIR principles, which describe how research data and other entities within the research lifecycle should be made Findable, Accessible, Interoperable, and Reusable (Wilkinson et al. 2016). Some of the goals of the FAIR-IMPACT project are related to working with PID service providers and infrastructures to better understand and meet user needs, align with the European Open Science Cloud (EOSC) PID policy, and maximize PID adoption. In the context of the project, these goals are addressed under a specific Work Package (WP) dedicated to PIDs. To achieve these goals, more coordination between PID service providers and EOSC is needed, resulting in PIDs for diverse research outputs including publications, data, software, instruments, services, people, and organisations. After establishing a joint value proposition by PID providers (Milestone 3.1 Joint value proposition by relevant PID providers), the next step is a proposal for a mechanism to support the necessary coordination. This report outlines the proposed coordination mechanism.
description: {"references": ["Mejias, Gabriela, Cousijn, Helena, Marjamaa-Mankinen, Liisa, van Lieshout, Natascha, Tatum, Clifford, & Lambert, Simon. (2023). M3.1 - Joint value proposition by relevant PID providers. Zenodo. https://doi.org/10.5281/zenodo.7798215", "Kalaitzi, Vasso, Dillo, Ingrid, Turner, Daniel, Ashley, Kevin, Davidson, Joy, Nordling, Josefine, Parland-von Essen, Jessica, Jonquet, Clement, Aubin, Sophie, Priddy, Mike, Verburg, Maaike, Fink, Anne Sofie, Rouchon, Olivier, Pittonet, Sara, Mari, Marialetizia, & Meneses, Rita. (2023). EOSC Policy Brief for FAIR-IMPACT. Zenodo. https://doi.org/10.5281/zenodo.8255645", "de Castro, Pablo, Herb, Ulrich, Rothfritz, Laura, & Sch\u00f6pfel, Joachim. (2023). Building the plane as we fly it: the promise of Persistent Identifiers. Zenodo. https://doi.org/10.5281/zenodo.7258286", "M. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, M. Blomberg, J.-W. Boiten, L.B. da Silva Santos, P.E. Bourne, et al. The FAIR guiding principles for scientific data management and stewardship. Sci. Data, 3 (2016), p. 160018 https://doi.org/10.1038/sdata.2016.18"]}
Bioexcel Deliverable 1.2 – First Project Release Of All Pilot Applications
Creators: name: Abraham, Mark
name: Ippoliti, Emiliano
name: Bonvin, Alexandre
name: de Groot, Bert
name: Soiland-Reyes, Stian
Publisher: name: Zenodo
Year: 2017
Subjects: Software
Software Engineering
HPC

description: This document describes the contents of the first project release of software

developed for pilot applications in BioExcel. The efforts of Work Package 1 are spread over the entire project timeframe, and some collaborations, deployments or benchmarks might also use preliminary new code. However, to establish known benchmark baselines and provide reference versions of all codes used in the project (e.g. to integrate them in BioExcel workflows and use by other BioExcel teams), the Work Package also makes these formal code releases. This also comes with records describing the current status of the software that results from the planning, development, documentation, and testing processes described

in Deliverable 1.1.

The release itself takes the form of a package of Open Source licensed

source code, and can be downloaded from the BioExcel webpage at

http://bioexcel.eu/software/code-repositories. For most of the codes this is a

BioExcel-specific repository to sync the releases with other project needs, while general users are usually recommended to follow the documentation, download and installation instructions available on the normal application web pages.
The new face of cigarette advertising: cigarette marketing strategies emerging after the MSA
Creators: name: Alexander, William
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: This thesis explores new advertising and promotional strategies cigarette manufacturers have developed and augmented since the 1998 Master Settlement Agreement (MSA). A literature review examines recent academic research on cigarette advertising strategies and smoking behavioral patterns. Three stories, written in the style of in-depth newspaper articles, each cover one new development. The first article discusses the growth of cigarette advertising and promotions at the point of sale, as well as how these promotions have affected how some retailers run their businesses. The second article explores cigarette promotions in bars and nightclubs and tells the story of one cigarette promotion in a Raleigh bar. The third article discusses flavored cigarettes and the legal challenges that they have faced since entering the mass market.
On the Nature and Origin of Atmospheric Annual and Semi-annual Oscillations
Creators: name: Courtillot, V.
name: Mouël, J-L. Le
name: Lopes, F.
name: Gibert, D.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: This paper proposes a joint analysis of variations of global sea-level pressure and of Earth's rotation (RP), expressed as the coordinates of the rotation pole and length of day. Sea-Level-Pressure (SLP) extracted components are a weak trend, eleven quasi-periodic or periodic components ($\sim$130, 90, 50, 22, 15, 4, 1.8 yr), an annual cycle and its first three harmonics. These periods are characteristic of the space-time evolution of the Earth's rotation axis and are present in many characteristic features of solar and terrestrial physics. We focus mainly on the annual and to a lesser extent semi-annual components. Maps of the first three components of SLP (that together comprise more than 85% of the data variance) reveal interesting symmetries. The trend is very stable and forms a triskel structure that can be modeled as Taylor-Couette flow of mode 3. The annual component is characterized by a large negative anomaly extending over Eurasia in the NH Summer (and the opposite in the NH Winter) and three large positive anomalies over Australia and the southern tips of South America and South Africa in the SH Spring (and the opposite in the SH Autumn) forming a triskel. The semi-annual component is characterized by three positive anomalies (an irregular triskel) in the NH Spring and Autumn (and the opposite in the NH Summer and Winter), and in the SH Spring and Autumn by a strong stable pattern consisting of three large negative anomalies forming a clear triskel within the 40$^{\circ}$-60$^{\circ}$ annulus formed by the southern oceans. A large positive anomaly centered over Antarctica, with its maximum displaced toward Australia, and a smaller one centered over Southern Africa complement the pattern.
Flow-Induced Buckling of Elastic Microfilaments with Non-Uniform Bending Stiffness
Creators: name: Nguyen, Thomas
name: Manikantan, Harishankar
Publisher: name: arXiv
Year: 2022
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Buckling plays a critical role in the transport and dynamics of elastic microfilaments in Stokesian fluids. However, previous work has only considered filaments with homogeneous structural properties. Filament backbone stiffness can be non-uniform in many biological systems like microtubules, where the association and disassociation of proteins can lead to spatial and temporal changes into structure. The consequences of such non-uniformities in the configurational stability and transport of these fibers are yet unknown. Here, we use slender-body theory and Euler-Bernoulli elasticity coupled with various non-uniform bending rigidity profiles to quantify this buckling instability using linear stability analysis and Brownian simulations. In shear flows, we observe more pronounced buckling in areas of reduced rigidity in our simulations. These areas of marked deformations give rise to differences in the particle extra stress, indicating a nontrivial rheological response due to the presence of these filaments. The fundamental mode shapes arising from each rigidity profile are consistent with the predictions from our linear stability analysis. Collectively, these results suggest that non-uniform bending rigidity can drastically alter fluid-structure interactions in physiologically relevant settings, providing a foundation to elucidate the complex interplay between hydrodynamics and the structural properties of biopolymers.
A Place at the Table: The Process of Personal and Community LGBT Engagement in the Gay Movement
Creators: name: Mundy, Dean E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Social movements are, by their very nature, public relations initiatives which exact change at the societal level. The modern American gay movement is no exception. Its leap onto America's front page is often marked by the Stonewall Riots of 1969. Indicative of most social movements, the gay experience has witnessed social unrest, community mobilization, and certainly push-back from a mainstream, heterocentric dominant culture. But as more critical battles are waged, and as more milestones are achieved, it is critical to analyze the current state of the gay movement "from within." Through a qualitative content-analysis and a series of in-depth interviews, this study attempts to define today's gay movement, analyze whose voices within the movement are being heard, and investigate the assumption of the "gay movement" as a traditional social movement. Ultimately, the research aims to determine how LGBT persons perceive the community's path to achieving a place at society's table.
Amplitude control of spin-triplet supercurrent in S/F/S Josephson junctions
Creators: name: Martinez, William
name: Pratt,, W. P.
name: Birge, Norman O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: Josephson junctions made with conventional s-wave superconductors and containing multiple layers of ferromagnetic materials can carry spin-triplet supercurrent in the presence of certain types of magnetic inhomogeneity. In junctions containing three ferromagnetic layers, the triplet supercurrent is predicted to be maximal when the magnetizations of adjacent layers are orthogonal, and zero when the magnetizations of any two adjacent layers are parallel. Here we demonstrate on-off control of the spin-triplet supercurrent in such junctions, achieved by rotating the magnetization direction of one of the three layers by 90$^{\circ}$. We obtain "on-off" ratios of 5, 7, and 19 for the supercurrent in the three samples studied so far. These observations directly confirm one of the most salient predictions of the theory, and pave the way for applications of spin-triplet Josephson junctions in the nascent area of "superconducting spintronics."
description: 5 pages, 4 figures
Electro-Mechanical Tuning of High-Q Bulk Acoustic Phonon Modes at Cryogenic Temperatures
Creators: name: Campbell, William M.
name: Galliou, Serge
name: Tobar, Michael E.
name: Goryachev, Maxim
Publisher: name: arXiv
Year: 2022
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: We investigate the electromechanical properties of quartz bulk acoustic wave resonators at extreme cryogenic temperatures. By applying a DC bias voltage, we demonstrate broad frequency tuning of high-Q phonon modes in a quartz bulk acoustic wave cavity at cryogenic temperatures of 4 K and 20 mK. More than 100 line-widths of tuning of the resonance peak without any degradation in loaded quality factor, which are as high as $1.73\times 10^9$, is seen for high order overtone modes. For all modes and temperatures the observed coefficient of frequency tuning is $\approx$ 3.5 mHz/V per overtone number $n$ corresponding to a maximum of 255.5 mHz/V for the $n = 73$ overtone mode. No degradation in the quality factor is observed for any value of applied biasing field.
description: 11 pages, 5 figures
Proposal for spin squeezing in rare-earth ion-doped crystals with a four-color scheme
Creators: name: Kriváchy, Tamás
name: Kaczmarek, Krzysztof T.
name: Afzelius, Mikael
name: Etesse, Jean
name: Haack, Géraldine
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Achieving spin squeezing within solid-state devices is a long standing research goal, due to the promise of their particularities, for instance their long coherence times, the possibility of low-temperature experiments or integration of entanglement-assisted sensors on-chip. In this work, we investigate an interferometer-free four-color scheme to achieve spin squeezing of rare-earth ion-doped crystals. The proposal relies on an analytic derivation that starts from a Tavis-Cummings model for light-matter interaction, providing microscopic insights onto spin-squeezing generation. We evidence spin squeezing signature in the light intensity variance. We consider the two particular cases of europium- and praseodymium-doped yttrium orthosilicates, workhorses of quantum technology developments. We show that up to 8 dB of spin squeezing can be obtained with readily accessible experimental resources, including noise due to photon scattering. Our results for rare-earth ion-doped crystals add to promising properties of these platforms for manipulating many-body entangled states and for high-precision measurements.
Realizability Models Separating Various Fan Theorems
Creators: name: Lubarsky, Robert S.
name: Rathjen, Michael
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03F50, 03F60, 03D80, 03C90

description: We develop a realizability model in which the realizers are the reals not just Turing computable in a fixed real but rather the reals in a countable ideal of Turing degrees. This is then applied to prove several separation results involving variants of the Fan Theorem.
BioExcel-2 Deliverable 2.6 – Integration of BioExcel software framework with standards and international initiatives
Creators: name: Soiland-Reyes, Stian
name: Hospital, Adam
name: Genís Bayarri
name: Niewelska, Ania
name: Cibin Sadasivan Baby
name: Lowe, Douglas
name: Andrio, Pau
name: Gelpi, Josep Ll.
Publisher: name: Zenodo
Year: 2021

description: This deliverable details the integration of the BioExcel computational framework with external initiatives and standards for the purpose of interoperability and portability, as well as wider FAIR aspects on discoverability and metadata. An ongoing challenge for users to take advantage of BioExcel tools in workflow management systems and across multiple compute infrastructures is to get the software installed and integrated into their system, without losing the significant optimization performance gains developed by BioExcel. Our work on forming the BioExcel Building Blocks (BioBB) have helped unify programmatic invocation of biomolecular simulation and modelling tools, making it easier to include them in major workflow systems in life sciences. Technically the building block functionality has been made possibly by building on multiple standards, technologies and initiatives for interoperability, as detailed in this deliverable. This document expands on how we have addressed Exascale challenges such as supporting multiple hardware-optimized binaries for execution on a variety of cloud compute environments. This is significant because the compute landscape has changed for BioExcel users towards a hybrid model of private clusters and public cloud usage. Workflows, which capture a computational method for reuse, need to be portable not just across these compute backends but also between different workflow systems. This is important to reliably apply a workflow through a wide range of scenarios: from training and prototyping, through development and customization towards scalable production runs. We have identified and generalized another advantage of what we call canonical workflow building blocks, that a conceptual workflow using a combination of
 blocks can be realized the same way in multiple workflow systems and give reproducible results, thanks to their common behaviour and underlying software packaging mechanisms. We show how our active engagement with ongoing initiatives have influenced
 WP2 development, publication of workflows and the BioExcel Building Blocks, as well as further evolved the standards themselves.
Decisions amid chaos: Jewish survival in Budapest, March 1944 - February 1945
Creators: name: Somogyi, Allison
Publisher: name: University of North Carolina at Chapel Hill
Year: 2014

description: The Jews of Budapest are completely apathetic and do virtually nothing to save themselves, Raoul Wallenberg stated bluntly in a dispatch written in July 1944. This simply was not the case. In fact, Jewish survival in World War II Budapest is a story of agency. A combination of knowledge, flexibility, and leverage, facilitated by the chaotic violence that characterized Budapest under Nazi occupation, helped to create an atmosphere in which survival tactics were common and widespread. This unique opportunity for agency helps to explain why approximately 58 percent of Budapest's 200,000 Jews survived the war while the total survival rate for Hungarian Jews was only 26 percent. Although unique, the experience of Jews within Budapest's city limits is not atypical and suggests that, when fortuitous circumstances provided opportunities for resistance, European Jews made informed decisions and employed everyday survival tactics that often made the difference between life and death.
Snowflake geometry in CAT(0) groups
Creators: name: Brady, Noel
name: Forester, Max
Publisher: name: arXiv
Year: 2016
Subjects: subject: Group Theory (math.GR)
subject: Geometric Topology (math.GT)
subject: FOS: Mathematics
subject: 20F65, 20F67, 20F69, 20E06, 57M07

description: We construct CAT(0) groups containing subgroups whose Dehn functions are given by $x^s$, for a dense set of numbers $s \in [2, \infty)$. This significantly expands the known geometric behavior of subgroups of CAT(0) groups.
description: 48 pages, 13 figures. v2: minor corrections; to appear in Journal of Topology
Constraints on Moon's orbit 3.2 billion years ago from tidal bundle data
Creators: name: Eulenfeld, Tom
name: Heubeck, Christoph
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The angular momentum of the Earth-Moon system was initially dominated by Earth's rotation with a short solar day of around 5 hours duration. Since then, Earth gradually transferred angular momentum through tidal friction to the orbit of the Moon, resulting in an increasing orbital radius and a deceleration of Earth's rotation. Geologic observations of tidal deposits can be used to verify and constrain models of lunar orbital evolution. In this work we reexamine the oldest tidal record suitable for analysis from the Moodies Group, South Africa, with an age of 3.22 billion years. Time frequency analysis of the series of thicknesses of the sandstone-shale layers yields a periodicity of 15.0 layers, taking into account the possibility of missing laminae. Assuming a mixed tidal system, the duration of two neap-spring-neap cycles was 30.0 lunar days for dominant semidiurnal or 30.0 sidereal days for dominant diurnal tides. We derive the relationship between this observation and the past Earth-Moon distance and re-visit related published work. We find that the Earth-Moon distance 3.2 billion years ago was about 70% of today's value. The Archean solar day was around 13 hours long. The ratio of solar to lunar tide-raising torque controls the leakage of angular momentum from the Earth-Moon system, but deviation from the assumed ratio of 0.211 results in only moderate changes. A duration of a postulated 21-hour atmospheric resonance shorter than 200 million years would be consistent with our observation; it would significantly alter Earth-Moon distance.
description: published in JGR: Planets, v3: published version
THE EFFECT OF MEN’S LACROSSE EQUIPMENT ON CHEST COMPRESSION AND VENTILATION DELIVERY
Creators: name: Davis, Mikaela
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Background: Current management guidelines for the care of equipped athletes in the case of cardiac emergencies are unclear regarding the decision to remove protective sports equipment prior to the delivery of cardiopulmonary resuscitation (CPR). It has been shown that the presence of football equipment decreases the effectiveness of CPR delivery. Our objective was to determine the effect of men’s lacrosse equipment on performing chest compressions and delivering adequate ventilations on patient simulators. Hypothesis: Conditions with more men’s lacrosse equipment left in place would decrease chest compression and ventilation efficacy for athletic trainers. Methods: Twenty-six certified athletic trainers participated in three different compression conditions and six different ventilation conditions using human patient simulators. Data for chest compressions (mean compression depth, compression rate, percentage of correctly released compressions, and percentage of adequate compressions) and ventilations (total ventilations, mean ventilation volume, and percentage of ventilations delivering adequate volume) were analyzed within subjects across each equipment condition. Results: The fully-equipped athlete was found to have the lowest mean compression depth (F2,50=26.57, p<0.001) and the fewest number of compressions reaching an adequate depth (F2,50=21.48, p<0.001) compared to all other conditions. The fully equipped athlete was also found to have the lowest mean ventilation volume (F2,125=17.79, p<0.001), and a lower percentage of ventilations reaching adequate volume (F2,125=43.05, p<0.001), in both one-person pocket mask and two-person bag valve mask scenarios. Conclusions: Our results indicate that chest compression and ventilation delivery are compromised in equipment-laden conditions in the sport of men’s lacrosse. As a result, in the case of a men’s lacrosse athlete requiring CPR, the shoulder pads must be lifted or cut away to expose the chest, and the facemask and chinstrap must be removed to access the airway.
Bacterial Characterization in Health and Periodontal Diseases During Induced Gingival Inflammation
Creators: name: Paes Batista da Silva, Andre
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Objective: to characterize the plaque bacteria in subjects enrolled in five biofilm-gingival interface (BGI) groups, and to determine whether re-institution of oral hygiene regimen would lead to a change in the biofilm composition. Methods: participants from each of the five BGI groups abstained from brushing and flossing teeth in two posterior sextants during a three week period. Participants reinstated normal oral hygiene (Day 21), and were followed for four weeks. Clinical parameters were recorded, and subgingival plaque samples were analyzed by the Human Oral Microbe Identification Microarray (HOMIM). Results: at baseline Synergystetes were more abundant in BGI-P2 and BGI-P3 than BGI-P1 and -G (p[less than or equal to]0.05). Overall, at the peak of induction there was an increase in levels of Firmicutes (p[less than or equal to]0.001), Fusobacteria (p=0.003), Proteobacteria (p ≤ 0.001), Synergistetes (p=0.04), and Bacteroidetes (p ≤ 0.001). At the resolution phase, the Synergistetes did not rebound. When analyzing each BGI group, plaque induced inflammation prompted distinguished changes in subgingival biofilm composition in most of the BGI groups except BGI-P3. Removal of plaque significantly reduced to baseline levels most bacteria in all BGI groups except a few bacterial phylum, such as Sinergistetes in BGI-P1, which were also detected in increased levels in the high pocket depth responders. Conclusions: it is indicated that the Synergistetes phylum may be highly involved in the progression of periodontal disease.
Ultrafast quantum key distribution using fully parallelized quantum channels
Creators: name: Terhaar, Robin
name: Rödiger, Jasper
name: Häußler, Matthias
name: Wahl, Michael
name: Gehring, Helge
name: Wolff, Martin A.
name: Beutel, Fabian
name: Hartmann, Wladick
name: Walter, Nicolai
name: Hanke, Jonas
name: Hanne, Peter
name: Walenta, Nino
name: Diedrich, Maximilian
name: Perlot, Nicolas
name: Tillmann, Max
name: Röhlicke, Tino
name: Ahangarianabhari, Mahdi
name: Schuck, Carsten
name: Pernice, Wolfram H. P.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: The field of quantum information processing offers secure communication protected by the laws of quantum mechanics and is on the verge of finding wider application for information transfer of sensitive data. To overcome the obstacle of inadequate cost-efficiency, extensive research is being done on the many components required for high data throughput using quantum key distribution (QKD). Aiming for an application-oriented solution, we report on the realization of a multichannel QKD system for plug-and-play high-bandwidth secure communication at telecom wavelength. For this purpose, a rack-sized multichannel superconducting nanowire single photon detector (SNSPD) system, as well as a highly parallelized time-correlated single photon counting (TCSPC) unit have been developed and linked to an FPGA-controlled QKD evaluation setup allowing for continuous operation and achieving high secret key rates using a coherent-one-way protocol.
description: 13 pages, 6 figures
Risk Taking
Creators: name: Gheriani, Gali
name: FELDMAN, DANA
name: Moscovitz, Amit
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: המחקר שלנו עוסק בהשפעה של מצב רוח ומהירות מחשבה על לקיחת סיכונים. זוהי הרשמה מראש למחקר שלנו במסגרת הקורס פסיכולוגיה ניסויית באוניברסיטת תל אביב.
Exometabolomic analysis of decidualizing human endometrial stromal and perivascular cells
Creators: name: Harden, Sarah
name: Zhou, Jieliang
name: Diniz-da-Costa, Maria
name: Lucas, Emma
name: Cui, Liang
name: Murakami, Keisuke
name: Fang, Jinling
name: Chen, Qingfeng
name: brosens, jan
name: Lee, Yie
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Life Sciences
subject: Decidualization
subject: endometrium
subject: Exometabolomics
subject: female reproduction
subject: perivascular
subject: stromal

description: Differentiation of endometrial fibroblasts into specialized decidual cells controls embryo implantation and transforms the cycling endometrium into a semi-permanent, immune-protective matrix that accommodates the placenta throughout pregnancy. This process starts during the midluteal phase of the menstrual cycle with decidual transformation of perivascular cells (PVC) surrounding the terminal spiral arterioles and endometrial stromal cells (EnSC) underlying the luminal epithelium. Decidualization involves extensive cellular reprogramming and acquisition of a secretory phenotype, essential for coordinated placental trophoblast invasion. Secreted metabolites are an emerging class of signalling molecules. Here, we used liquid chromatography-mass spectrometry to characterise the dynamic changes in metabolite secretion (exometabolome) of primary PVC and EnSC decidualized over 8 days. We identified 79 annotated metabolites differentially secreted upon decidualization, including prostaglandin, sphingolipid, and hyaluronic acid metabolites. Secreted metabolites encompassed 21 metabolic pathways, most prominently glycerolipid and pyrimidine metabolism. Although temporal exometabolome changes were comparable between decidualizing PVC and EnSC, 32 metabolites were differentially secreted across the decidualization time-course. Further, targeted metabolomics demonstrated a conspicuous difference in xanthine secretion between decidualized PVC and EnSC. Taken together, our findings indicate that the metabolic footprints generated by different decidual subpopulations encode spatiotemporal information that may be important for optimal embryo implantation.
The warm ionized gas in CALIFA early-type galaxies: 2D emission-line patterns and kinematics for 32 galaxies
Creators: name: Gomes, J. M.
name: Papaderos, P.
name: Kehrig, C.
name: Vílchez, J. M.
name: Lehnert, M. D.
name: Sánchez, S. F.
name: Ziegler, B.
name: Breda, I.
name: Reis, S. N. dos
name: Iglesias-Páramo, J.
name: Bland-Hawthorn, J.
name: Galbany, L.
name: Bomans, D. J.
name: Rosales-Ortega, F. F.
name: Fernandes, R. Cid
name: Walcher, C. J.
name: Falcón-Barroso, J.
name: García-Benito, R.
name: Márquez, I.
name: del Olmo, A.
name: Masegosa, J.
name: Mollá, M.
name: Marino, R. A.
name: Delgado, R. M. González
name: López-Sánchez, Á. R.
name: collaboration, the CALIFA
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The morphological, spectroscopic and kinematical properties of the warm interstellar medium (wim) in early-type galaxies (ETGs) hold key observational constraints to nuclear activity and the buildup history of these massive, quiescent systems. High-quality integral field spectroscopy (IFS) data with a wide spectral and spatial coverage, such as those from the CALIFA survey, offer an unprecedented opportunity for advancing our understanding of the wim in ETGs. This article centers on a 2D investigation of the wim component in 32 nearby (
description: Accepted to A&A, 59 pages, 1 Table, 46 figures
Tunneling method for Hawking radiation in the Nariai case
Creators: name: Belgiorno, F.
name: Cacciatori, S. L.
name: Piazza, F. Dalla
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We revisit the tunneling picture for the Hawking effect in light of the charged Nariai manifold, because this general relativistic solution, which displays two horizons, provides the bonus to allow the knowledge of exact solutions of the field equations. We first perform a revisitation of the tunneling ansatz in the framework of particle creation in external fields a la Nikishov, which corroborates the interpretation of the semiclassical emission rate Gamma as the conditional probability rate for the creation of a couple of particles from the vacuum. Then, particle creation associated with the Hawking effect on the Nariai manifold is calculated in two ways. On the one hand, we apply the Hamilton Jacobi formalism for tunneling, in the case of a charged scalar field on the given background. On the other hand, the knowledge of the exact solutions for the Klein Gordon equations on Nariai manifold, and their analytic properties on the extended manifold, allow us a direct computation of the flux of particles leaving the horizon, and, as a consequence, we obtain a further corroboration of the semiclassical tunneling picture from the side of S-matrix formalism.
description: 11 pages. Revised version, published in Gen. Rel. Grav
Point-particle drag, lift, and torque closure models using machine learning: hierarchical approach and interpretability
Creators: name: Siddani, B.
name: Balachandar, S.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Developing deterministic neighborhood-informed point-particle closure models using machine learning has garnered interest in recent times from dispersed multiphase flow community. The robustness of neural models for this complex multi-body problem is hindered by the availability of particle-resolved data. The present work addresses this unavoidable limitation of data paucity by implementing two strategies: (i) by using a rotation and reflection equivariant neural network and (ii) by pursuing a physics-based hierarchical machine learning approach. The resulting machine learned models are observed to achieve a maximum accuracy of 85% and 96% in the prediction of neighbor-induced force and torque fluctuations, respectively, for a wide range of Reynolds number and volume fraction conditions considered. Furthermore, we pursue force and torque network architectures that provide universal prediction spanning a wide range of Reynolds number ($0.25 \leq Re \leq 250$) and particle volume fraction ($0 \leq ϕ\leq 0.4$). The hierarchical nature of the approach enables improved prediction of quantities such as streamwise torque, by going beyond binary interactions to include trinary interactions.
BioExcel-2 Deliverable D1.6 – Final project release
Creators: name: Hess, Berk
name: Proeme, Arno
name: Morozov, Dmitry
name: Bonvin, Alexandre
name: Vargas Honorato, Rodrigo
name: Gapsys, Vytautas
name: de Groot, Bert
Publisher: name: Zenodo
Year: 2022

description: This document describes the contents of the fourth project release (second in BioExcel-2), of software developed for the core applications in BioExcel. In addition to describing the final releases in BioExcel-2 for the core applications, this document also presents what has been achieved in terms of features and performance for the codes over the entire project timeframe. To provide reference versions of all codes used in the project (e.g. to integrate them in BioExcel workflows and use by other BioExcel teams), the Work Package also makes these formal code releases. This also comes with records describing the current status of the software that results from the planning, development, documentation, and testing processes. The release itself takes the form of a package of Open Source licensed source code with accompanying documentation, tests, benchmarks, and benchmark reports and can be downloaded from https://doi.org/10.5281/zenodo.6761700 or from the BioExcel webpage at http://bioexcel.eu/software/code-repositories. All codes (apart from CP2K whose core development team is external to BioExcel) have now timed the BioExcel release to be in sync with the individual product releases, so there is less confusion for the users, as well as less maintenance and documentation overhead for the developers.
New family of simple $\mathfrak{gl}_{2n}(\mathbb{C})$-modules
Creators: name: Nilsson, Jonathan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Representation Theory (math.RT)
subject: FOS: Mathematics

description: We construct a new family of simple $\mathfrak{gl}_{2n}$-modules which depends on $n^2$ generic parameters. Each such module is isomorphic to the regular $U(\mathfrak{gl}_{n})$-module when restricted the $\mathfrak{gl}_{n}$-subalgebra naturally embedded into the top-left corner.
description: 17 pages
On the efficacy of the wisdom of crowds to forecast economic indicators
Creators: name: Neto, Nilton S. Siqueira
name: Fontanari, José F.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Physical sciences

description: The interest in the wisdom of crowds stems mainly from the possibility of combining independent forecasts from experts in the hope that many expert minds are better than a few. Hence the relevant subject of study nowadays is the Vox Expertorum rather than Galton's original Vox Populi. Here we use the Federal Reserve Bank of Philadelphia's Survey of Professional Forecasters to analyze $15455$ forecasting contests to predict a variety of economic indicators. We find that the median has advantages over the mean as a method to combine the experts' estimates: the odds that the crowd beats all participants of a forecasting contest is $0.015$ when the aggregation is given by the mean and $0.026$ when it is given by the median. In addition, the median is always guaranteed to beat the majority of the participants, whereas the mean beats that majority in 67 percent of the forecasts only. Both aggregation methods yield a $20$ percent error on the average, which must be contrasted with the $15$ percent error of the contests' winners. A standard time series forecasting algorithm, the ARIMA model, yields a $31$ percent error on the average. However, since the expected error of a randomly selected forecaster is about $22$ percent, our conclusion is that selective attention is the most likely explanation for the mysterious high accuracy of the crowd reported in the literature.
Curvature and torsion effects in the spin-current driven domain wall motion
Creators: name: Yershov, Kostiantyn V.
name: Kravchuk, Volodymyr P.
name: Sheka, Denis D.
name: Gaididei, Yuri
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The domain wall motion along a helix-shaped nanowire is studied for the case of spin-current driving via Bazaliy-Zhang-Li mechanism. The analysis is based on collective variable approach. Two new effects are ascertained: (i) the curvature results in appearance of the Walker limit for a uniaxial wire, (ii) the torsion results in effective shift of the nonadiabatic spin torque parameter $β$. The latter effect changes considerably the domain wall velocity and can result in negative domain wall mobility. This effect can be also used for an experimental determination of the nonadiabatic parameter $β$ and damping coefficient $α$.
On the Slow Drift of Solstices: Milankovic Cycles and Mean Global Temperature
Creators: name: Lopes, F.
name: Courtillot, V.
name: Gibert, D.
name: Mouël, J-L. Le
Publisher: name: arXiv
Year: 2022
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Geophysics (physics.geo-ph)
subject: FOS: Physical sciences

description: The Earth's revolution is modified by changes in inclination of its rotation axis. Despite the fact that the gravity field is central, the Earth's trajectory is not closed and the equinoxes drift. Milankovic (1920) argued that the shortest precession period of solstices is 20,7kyr: the Summer solstice in one hemisphere takes place alternately every 11kyr at perihelion and at aphelion. We have submitted the time series for the Earth's pole of rotation, global mean surface temperature and ephemeris to iterative Singular Spectrum Analysis. iSSA extracts from each a trend, a 1yr and a 60yr component. Both the apparent drift of solstices of Earth around the Sun and the global mean temperature exhibit a strong 60yr oscillation. The "fixed dates" of solstices actually drift. Comparing the time evolution of the Winter and Summer solstices positions of the rotation pole and the first iSSA component (trend) of the temperature allows one to recognize some common features. A basic equation from Milankovic links the derivative of heat received at a given location on Earth to solar insolation, known functions of the location coordinates, solar declination and hour angle, with an inverse square dependence on the Sun-Earth distance. We have translated the drift of solstices as a function of distance to the Sun into the geometrical insolation theory of Milankovic. Shifting the inverse square of the 60yr iSSA drift of solstices by 15 years with respect to the first derivative of the 60yr iSSA trend of temperature, that is exactly a quadrature in time, puts the two curves in quasi-exact superimposition. The probability of a chance coincidence appears very low. Correlation does not imply causality when there is no accompanying model. Here Milankovic's equation can be considered as a model that is widely accepted. This paper identifies a case of agreement between observations and a mathematical formulation.
Scheduling rules to minimize total tardiness in a parallel machine problem with setup and calendar constraints
Creators: name: Lamothe, Jacques
name: Marmier, François
name: Dupuy, Matthieu
name: Gaborit, Paul
name: Dupont, Lionel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences

description: Quality control lead times are one of most significant causes of loss of time in the pharmaceutical and cosmetics industries. This is partly due to the organization of laboratories that feature parallel multipurpose machines for chromatographic analyses. The testing process requires long setup times and operators are needed to launch the process. The various controls are non-preemptive and are characterized by a release date, a due date and available routings. These quality processes lead to significant delays, and we therefore evaluate the total tardiness criterion. Previous heuristics were defined for the total tardiness criterion, parallel machines, and setup such as ATC (Apparent Tardiness Cost) and ATCS (ATC with setups). We propose new rules and a simulated annealing procedure in order to minimize total tardiness.